Diagnostics and therapeutics for diseases associated with 5-hydroxytryptamine 1f receptor (5-ht1f)

ABSTRACT

The invention provides a human 5-HT1F which is associated with the hematological diseases, disorders of the peripheral and central nervous system, gastrointestinal diseases, cardiovascular diseases, cancer, muscle/skeleton disorders, respiratory diseases and urological diseases. The invention also provides assays for the identification of compounds useful in the treatment or prevention of hematological diseases, disorders of the peripheral and central nervous system, gastrointestinal diseases, cardiovascular diseases, cancer, muscle/skeleton disorders, respiratory diseases and urological diseases. The invention also features compounds which bind to and/or activate or inhibit the activity of 5-HT1F as well as pharmaceutical compositions comprising such compounds.

TECHNICAL FIELD OF THE INVENTION

The present invention is in the field of molecular biology, moreparticularly, the present invention relates to nucleic acid sequencesand amino acid sequences of a human 5-HT1F and its regulation for thetreatment of hematological diseases, disorders of the peripheral andcentral nervous system, gastrointestinal diseases, cardiovasculardiseases, cancer, muscle/skeleton disorders, respiratory diseases andurological diseases in mammals.

BACKGROUND OF THE INVENTION

G-Protein Coupled Receptors

5-HT1F is a seven transmembrane G protein coupled receptor (GPCR)[McAllister et al., (1992), Adham et al., (1993), Adham et al. (1994)].Many medically significant biological processes are mediated by signaltransduction pathways that involve G-proteins [Lefkowitz, (1991)]. Thefamily of G-protein coupled receptors (GPCRs) includes receptors forhormones, neurotransmitters, growth factors, and viruses. Specificexamples of GPCRs include receptors for such diverse agents as dopamine,calcitonine, adrenergic hormones, endotheline, cAMP, adenosine,acetylcholine, serotonine, histamine, thrombin, kinine, folliclestimulating hormone, opsins, endothelial differentiation gene-1,rhodopsins, odorants, cytomegalovirus, G-proteins themselves, effectorproteins such as phospholipase C, adenyl cyclase, and phosphodiesterase,and actuator proteins such as protein kinase A and protein kinase C.

GPCRs possess seven conserved membrane-spanning domains connecting atleast eight divergent hydrophilic loops. GPCRs, also known as seventransmembrane, 7TM, receptors, have been characterized as includingthese seven conserved hydrophobic stretches of about 20 to 30 aminoacids, connecting at least eight divergent hydrophilic loops. Most GPCRshave single conserved cysteine residues in each of the first twoextracellular loops, which form disulfide bonds that are believed tostabilize functional protein structure. The seven transmembrane regionsare designated as TM1, TM2, TM3, TM4, TM5, TM6, and TM7. TM3 is beingimplicated with signal transduction. Phosphorylation and lipidation(palitylation or farnesylation) of cysteine residues can influencesignal transduction of some GPCRs. Most GPCRs contain potentialphosphorylation sites within the third cytoplasmic loop and/or thecarboxy terminus. For several GPCRs, such as the beta-adrenergicreceptor, phosphorylation by protein kinase A and/or specific receptorkinases mediates receptor desensitization.

For some receptors, the ligand binding sites of GPCRs are believed tocomprise hydrophilic sockets formed by several GPCR transmembranedomains. The hydrophilic sockets are surrounded by hydrophobic residuesof the GPCRs. The hydrophilic side of each GPCR transmembrane helix ispostulated to face inward and form a polar ligand binding site. TM3 isbeing implicated with several GPCRs as having a ligand binding site,such as the TM3 aspartate residue. TM5 serines, a TM6 asparagine, andTM6 or TM7 phenylalanines or tyrosines also are implicated in ligandbinding.

GPCRs are coupled inside the cell by heterotrimeric G-proteins tovarious intracellular enzymes, ion channels, and transporters. DifferentG-protein alpha-subunits preferentially stimulate particular effectorsto modulate various biological functions in a cell. Phosphorylation ofcytoplasmic residues of GPCRs is an important mechanism for theregulation of some GPCRs. For example, in one form of signaltransduction, the effect of hormone binding is the activation of theenzyme, adenylate cyclase, inside the cell. Enzyme activation byhormones is dependent on the presence of the nucleotide GTP. GTP alsoinfluences hormone binding. A G-protein connects the hormone receptor toadenylate cyclase. G-protein exchanges GTP for bound GDP when activatedby a hormone receptor. The GTP-carrying form then binds to activatedadenylate cyclase. Hydrolysis of GTP to GDP, catalyzed by the G-proteinitself, returns the G-protein to its basal, inactive form. Thus, theG-protein serves a dual role, as an intermediate that relays the signalfrom receptor to effector, and as a clock that controls the duration ofthe signal.

Over the past 15 years, nearly 350 therapeutic agents targeting 7TMreceptors have been successfully introduced into the market. Thisindicates that these receptors have an established, proven history astherapeutic targets. Clearly, there is a need for identification andcharacterization of further receptors which can play a role inpreventing, ameliorating, or correcting dysfunctions or diseasesincluding, but not limited to, infections such as bacterial, fungal,protozoan, and viral infections, particularly those caused by HIVviruses, cancers, allergies including asthma, cardiovascular diseasesincluding acute heart failure, hypotension, hypertension, anginapectoris, myocardial infarction, hematological diseases, genito-urinarydiseases including urinary incontinence and benign prostate hyperplasia,osteoporosis, and peripheral and central nervous system disordersincluding pain, Alzheimer's disease and Parkinson's disease.

TaqMan-Technology/Expression Profiling

TaqMan is a recently developed technique, in which the release of afluorescent reporter dye from a hybridisation probe in real-time duringa polymerase chain reaction (PCR) is proportional to the accumulation ofthe PCR product. Quantification is based on the early, linear part ofthe reaction, and by determining the threshold cycle (CT), at whichfluorescence above background is first detected.

Gene expression technologies may be useful in several areas of drugdiscovery and development, such as target identification, leadoptimization, and identification of mechanisms of action. The TaqMantechnology can be used to compare differences between expressionprofiles of normal tissue and diseased tissue. Expression profiling hasbeen used in identifying genes, which are up- or downregulated in avariety of diseases. An interesting application of expression profilingis temporal monitoring of changes in gene expression during diseaseprogression and drug treatment or in patients versus healthyindividuals. The premise in this approach is that changes in pattern ofgene expression in response to physiological or environmental stimuli(e.g., drugs) may serve as indirect clues about disease-causing genes ordrug targets. Moreover, the effects of drugs with established efficacyon global gene expression patterns may provide a guidepost, or a geneticsignature, against which a new drug candidate can be compared.

5-HT1F

The nucleotide sequence of 5-HT1F is accessible in public databases bythe accession number NM_(—)000866 and is given in SEQ ID NO:1. The aminoacid sequence of 5-HT1F is depicted in SEQ ID NO:2.

Serotonin (5-hydroxytryptamine; 5-HT) is a neurotransmitter thought toplay a role in various cognitive and behavioral functions includingfeeding, sleep, pain, depression, and learning. Serotonin receptors havebeen divided into 4 classes designated 5-Hr-1-like, 5-HT-2,5-HT-3, and5-HT-4, depending on their ligand binding and effector-couplingproperties. Tthe 5-HT-1 receptor family can be further subdivided into 5subtypes, 5-HT-1A to 5-HT-1F [McAllister et al., (1992); Adham et al.,(1993)]. The expression of 5-HT1F in brian is described in Adham et al.,1994. The 5-HT1F receptor is also decribed in patents

5-HT1F shows the highest homology to the human receptor GPR42 receptoras shown in example 1.

SUMMARY OF THE INVENTION

The invention relates to novel disease associations of 5-HT1Fpolypeptides and polynucleotides. The invention also relates to novelmethods of screening for therapeutic agents for the treatment ofhematological diseases, disorders of the peripheral and central nervoussystem, gastrointestinal diseases, cardiovascular diseases, cancer,muscle/skeleton disorders, respiratory diseases and urological diseasesin a mammal. The invention also relates to pharmaceutical compositionsfor the treatment of hematological diseases, disorders of the peripheraland central nervous system, gastrointestinal diseases, cardiovasculardiseases, cancer, muscle/skeleton disorders, respiratory diseases andurological diseases in a mammal comprising a 5-HT1F polypeptide, a5-HT1F polynucleotide, or regulators of 5-HT1F or modulators of 5-HT1Factivity. The invention further comprises methods of diagnosinghematological diseases, disorders of the peripheral and central nervoussystem, gastrointestinal diseases, cardiovascular diseases, cancer,muscle/skeleton disorders, respiratory diseases and urological diseasesin a mammal.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows the nucleotide sequence of a 5-HT1F receptor polynucleotide(SEQ ID NO:1).

FIG. 2 shows the amino acid sequence of a 5-HT1F receptor polypeptide(SEQ ID NO:2).

FIG. 3 shows the nucleotide sequence of a primer useful for theinvention (SEQ ID NO:3).

FIG. 4 shows the nucleotide sequence of a primer useful for theinvention (SEQ ID NO:4).

FIG. 5 shows a nucleotide sequence useful as a probe to detect proteinsof the invention (SEQ ID NO:5).

DETAILED DESCRIPTION OF THE INVENTION

Definition of Terms

An “oligonucleotide” is a stretch of nucleotide residues which has asufficient number of bases to be used as an oligomer, amplimer or probein a polymerase chain reaction (PCR). Oligonucleotides are prepared fromgenomic or cDNA sequence and are used to amplify, reveal, or confirm thepresence of a similar DNA or RNA in a particular cell or tissue.Oligonucleotides or oligomers comprise portions of a DNA sequence havingat least about 10 nucleotides and as many as about 35 nucleotides,preferably about 25 nucleotides.

“Probes” may be derived from naturally occurring or recombinant single-or double-stranded nucleic acids or may be chemically synthesized. Theyare useful in detecting the presence of identical or similar sequences.Such probes may be labeled with reporter molecules using nicktranslation, Klenow fill-in reaction, PCR or other methods well known inthe art. Nucleic acid probes may be used in southern, northern or insitu hybridizations to determine whether DNA or RNA encoding a certainprotein is present in a cell type, tissue, or organ.

A “fragment of a polynucleotide” is a nucleic acid that comprises all orany part of a given nucleotide molecule, the fragment having fewernucleotides than about 6 kb, preferably fewer than about 1 kb.

“Reporter molecules” are radionuclides, enzymes, fluorescent,chemiluminescent, or chromogenic agents which associate with aparticular nucleotide or amino acid sequence, thereby establishing thepresence of a certain sequence, or allowing for the quantification of acertain sequence.

“Chimeric” molecules may be constructed by introducing all or part ofthe nucleotide sequence of this invention into a vector containingadditional nucleic acid sequence which might be expected to change anyone or several of the following 5-HT1F characteristics: cellularlocation, distribution, ligand-binding affinities, interchainaffinities, degradation/turnover rate, signaling, etc.

“Active”, with respect to a 5-HT1F polypeptide, refers to those forms,fragments, or domains of a 5-HT1F polypeptide which retain thebiological and/or antigenic activity of a 5-HT1F polypeptide.

“Naturally occurring 5-HT1F polypeptide” refers to a polypeptideproduced by cells which have not been genetically engineered andspecifically contemplates various polypeptides arising frompost-translational modifications of the polypeptide including but notlimited to acetylation, carboxylation, glycosylation, phosphorylation,lipidation and acylation.

“Derivative” refers to polypeptides which have been chemically modifiedby techniques such as ubiquitination, labeling (see above), pegylation(derivatization with polyethylene glycol), and chemical insertion orsubstitution of amino acids such as ornithine which do not normallyoccur in human proteins.

“Conservative amino acid substitutions” result from replacing one aminoacid with another having similar structural and/or chemical properties,such as the replacement of a leucine with an isoleucine or valine, anaspartate with a glutamate, or a threonine with a serine.

“Insertions” or “deletions” are typically in the range of about 1 to 5amino acids. The variation allowed may be experimentally determined byproducing the peptide synthetically while systematically makinginsertions, deletions, or substitutions of nucleotides in the sequenceusing recombinant DNA techniques.

A “signal sequence” or “leader sequence” can be used, when desired, todirect the polypeptide through a membrane of a cell. Such a sequence maybe naturally present on the polypeptides of the present invention orprovided from heterologous sources by recombinant DNA techniques.

An “oligopeptide” is a short stretch of amino acid residues and may beexpressed from an oligonucleotide. Oligopeptides comprise a stretch ofamino acid residues of at least 3, 5, 10 amino acids and at most 10, 15,25 amino acids, typically of at least 9 to 13 amino acids, and ofsufficient length to display biological and/or antigenic activity.

“Inhibitor” is any substance which retards or prevents a chemical orphysiological reaction or response. Common inhibitors include but arenot limited to antisense molecules, antibodies, and antagonists.

“Standard expression” is a quantitative or qualitative measurement forcomparison. It is based on a statistically appropriate number of normalsamples and is created to use as a basis of comparison when performingdiagnostic assays, running clinical trials, or following patienttreatment profiles.

“Animal” as used herein may be defined to include human, domestic (e.g.,cats, dogs, etc.), agricultural (e.g., cows, horses, sheep, etc.) ortest species (e.g., mouse, rat, rabbit, etc.).

A “5-HT1F polynucleotide”, within the meaning of the invention, shall beunderstood as being a nucleic acid molecule selected from a groupconsisting of

-   (i) nucleic acid molecules encoding a polypeptide comprising the    amino acid sequence of SEQ ID NO: 2,-   (ii) nucleic acid molecules comprising the sequence of SEQ ID NO: 1,-   (iii) nucleic acid molecules having the sequence of SEQ BD NO: 1,-   (iv) nucleic acid molecules the complementary strand of which    hybridizes under stringent conditions to a nucleic acid molecule of    (i), (ii), or (iii); and-   (v) nucleic acid molecules the sequence of which differs from the    sequence of a nucleic acid molecule of (iii) due to the degeneracy    of the genetic code;    wherein the polypeptide encoded by said nucleic acid molecule has    5-HT1F activity.

A “5-HT1F polypeptide”, within the meaning of the invention, shall beunderstood as being a polypeptide selected from a group consisting of

-   (i) polypeptides having the sequence of SEQ ID NO: 2,-   (ii) polypeptides comprising the sequence of SEQ ID NO: 2,-   (iii) polypeptides encoded by 5-HT1F polynucleotides; and-   (iv) polypeptides which show at least 99%, 98%, 95%, 90%, or 80%    homology with a polypeptide of (i), (ii), or (iii);    wherein said polypeptide has 5-HT1F activity.

The nucleotide sequences encoding a 5-HT1F (or their complement) havenumerous applications in techniques known to those skilled in the art ofmolecular biology.

These techniques include use as hybridization probes, use in theconstruction of oligomers for PCR, use for chromosome and gene mapping,use in the recombinant production of 5-HT1F, and use in generation ofantisense DNA or RNA, their chemical analogs and the like. Uses ofnucleotides encoding a 5-HT1F disclosed herein are exemplary of knowntechniques and are not intended to limit their use in any techniqueknown to a person of ordinary skill in the art. Furthermore, thenucleotide sequences disclosed herein may be used in molecular biologytechniques that have not yet been developed, provided the new techniquesrely on properties of nucleotide sequences that are currently known,e.g., the triplet genetic code, specific base pair interactions, etc.

It will be appreciated by those skilled in the art that as a result ofthe degeneracy of the genetic code, a multitude of 5-HT1F—encodingnucleotide sequences may be produced. Some of these will only bearminimal homology to the nucleotide sequence of the known and naturallyoccurring 5-HT1F. The invention has specifically contemplated each andevery possible variation of nucleotide sequence that could be made byselecting combinations based on possible codon choices. Thesecombinations are made in accordance with the standard triplet geneticcode as applied to the nucleotide sequence of naturally occurring5-HT1F, and all such variations are to be considered as beingspecifically disclosed.

Although the nucleotide sequences which encode a 5-HT1F, its derivativesor its variants are preferably capable of hybridizing to the nucleotidesequence of the naturally occurring 5-HT1F polynucleotide understringent conditions, it may be advantageous to produce nucleotidesequences encoding 5-HT1F polypeptides or its derivatives possessing asubstantially different codon usage. Codons can be selected to increasethe rate at which expression of the peptide occurs in a particularprokaryotic or eukaryotic expression host in accordance with thefrequency with which particular codons are utilized by the host. Otherreasons for substantially altering the nucleotide sequence encoding a5-HT1F polypeptide and/or its derivatives without altering the encodedamino acid sequence include the production of RNA transcripts havingmore desirable properties, such as a greater half-life, than transcriptsproduced from the naturally occurring sequence.

Nucleotide sequences encoding a 5-HT1F polypeptide may be joined to avariety of other nucleotide sequences by means of well establishedrecombinant DNA techniques. Useful nucleotide sequences for joining to5-HT1F polynucleotides include an assortment of cloning vectors such asplasmids, cosmids, lambda phage derivatives, phagemids, and the like.Vectors of interest include expression vectors, replication vectors,probe generation vectors, sequencing vectors, etc. In general, vectorsof interest may contain an origin of replication functional in at leastone organism, convenient restriction endonuclease sensitive sites, andselectable markers for one or more host cell systems.

Another aspect of the subject invention is to provide for5-HT1F-specific hybridization probes capable of hybridizing withnaturally occurring nucleotide sequences encoding 5-HT1F. Such probesmay also be used for the detection of similar GPCR encoding sequencesand should preferably show at least 40% nucleotide identity to 5-HT1Fpolynucleotides. The hybridization probes of the subject invention maybe derived from the nucleotide sequence presented as SEQ ID NO:1 or fromgenomic sequences including promoter, enhancers or introns of the nativegene. Hybridization probes may be labelled by a variety of reportermolecules using techniques well known in the art.

It will be recognized that many deletional or mutational analogs of5-HT1F polynucleotides will be effective hybridization probes for 5-HT1Fpolynucleotides. Accordingly, the invention relates to nucleic acidsequences that hybridize with such 5-HT1F encoding nucleic acidsequences under stringent conditions.

“Stringent conditions” refers to conditions that allow for thehybridization of substantially related nucleic acid sequences. Forinstance, such conditions will generally allow hybridization of sequencewith at least about 85% sequence identity, preferably with at leastabout 90% sequence identity, more preferably with at least about 95%sequence identity. Hybridization conditions and probes can be adjustedin well-characterized ways to achieve selective hybridization ofhuman-derived probes. Stringent conditions, within the meaning of theinvention are 65° C. in a buffer containing 1 mM EDTA, 0.5 M NaHPO₄ (pH7.2), 7% (w/v) SDS.

Nucleic acid molecules that will hybridize to 5-HT1F polynucleotidesunder stringent conditions can be identified functionally. Withoutlimitation, examples of the uses for hybridization probes include:histochemical uses such as identifying tissues that express 5-HT1F;measuring mRNA levels, for instance to identify a sample's tissue typeor to identify cells that express abnormal levels of 5-HT1F; anddetecting polymorphisms of 5-HT1F.

PCR provides additional uses for oligonucleotides based upon thenucleotide sequence which encodes 5-HT1F. Such probes used in PCR may beof recombinant origin, chemically synthesized, or a mixture of both.Oligomers may comprise discrete nucleotide sequences employed underoptimized conditions for identification of 5-HT1F in specific tissues ordiagnostic use. The same two oligomers, a nested set of oligomers, oreven a degenerate pool of oligomers may be employed under less stringentconditions for identification of closely related DNAs or RNAs.

Rules for designing polymerase chain reaction (PCR) primers are nowestablished, as reviewed by PCR Protocols. Degenerate primers, i.e.,preparations of primers that are heterogeneous at given sequencelocations, can be designed to amplify nucleic acid sequences that arehighly homologous to, but not identical with 5-HT1F. Strategies are nowavailable that allow for only one of the primers to be required tospecifically hybridize with a known sequence. For example, appropriatenucleic acid primers can be ligated to the nucleic acid sought to beamplified to provide the hybridization partner for one of the primers.In this way, only one of the primers need be based on the sequence ofthe nucleic acid sought to be amplified.

PCR methods for amplifying nucleic acid will utilize at least twoprimers. One of these primers will be capable of hybridizing to a firststrand of the nucleic acid to be amplified and of priming enzyme-drivennucleic acid synthesis in a first direction. The other will be capableof hybridizing the reciprocal sequence of the first strand (if thesequence to be amplified is single stranded, this sequence willinitially be hypothetical, but will be synthesized in the firstamplification cycle) and of priming nucleic acid synthesis from, thatstrand in the direction opposite the first direction and towards thesite of hybridization for the first primer. Conditions for conductingsuch amplifications, particularly under preferred stringenthybridization conditions, are well known.

Other means of producing specific hybridization probes for 5-HT1Finclude the cloning of nucleic acid sequences encoding 5-HT1F or 5-HT1Fderivatives into vectors for the production of mRNA probes. Such vectorsare known in the art, are commercially available and may be used tosynthesize RNA probes in vitro by means of the addition of theappropriate RNA polymerase as T7 or SP6 RNA polymerase and theappropriate reporter molecules.

It is possible to produce a DNA sequence, or portions thereof, entirelyby synthetic chemistry. After synthesis, the nucleic acid sequence canbe inserted into any of the many available DNA vectors and theirrespective host cells using techniques which are well known in the art.Moreover, synthetic chemistry may be used to introduce mutations intothe nucleotide sequence. Alternately, a portion of sequence in which amutation is desired can be synthesized and recombined with longerportion of an existing genomic or recombinant sequence.

5-HT1F polynucleotides may be used to produce a purified oligo-orpolypeptide using well known methods of recombinant DNA technology. Theoligopeptide may be expressed in a variety of host cells, eitherprokaryotic or eukaryotic. Host cells may be from the same species fromwhich the nucleotide sequence was derived or from a different species.Advantages of producing an oligonucleotide by recombinant DNA technologyinclude obtaining adequate amounts of the protein for purification andthe availability of simplified purification procedures.

Quantitative Determinations of Nucleic Acids

An important step in the molecular genetic analysis of human disease isoften the enumeration of the copy number of a nucleis acid or therelative expression of a gene in particular tissues. Several differentapproaches are currently available to make quantitative determinationsof nucleic acids. Chromosome-based techniques, such as comparativegenomic hybridization (CGH) and fluorescent in situ hybridization (FISH)facilitate efforts to cytogenetically localize genomic regions that arealtered in tumor cells. Regions of genomic alteration can be narrowedfurther using loss of heterozygosity analysis (LOH), in which diseaseDNA is analyzed and compared with normal DNA for the loss of aheterozygous polymorphic marker. The first experiments used restrictionfragment length polymorphisms (RFLPs) [Johnson, (1989)], orhypervariable mini-satellite DNA [Barnes, 2000]. In recent years LOH hasbeen performed primarily using PCR amplification of microsatellitemarkers and electrophoresis of the radio labelled [Jeffreys, (1985)] orfluorescently labelled PCR products [Weber, (1990)] and compared betweenpaired normal and disease DNAs.

A number of other methods have also been developed to quantify nucleicacids [Gergen, (1992)]. More recently, PCR and RT-PCR methods have beendeveloped which are capable of measuring the amount of a nucleic acid ina sample. One approach, for example, measures PCR product quantity inthe log phase of the reaction before the formation of reaction productsplateaus [Thomas, (1980)].

A gene sequence contained in all samples at relatively constant quantityis typically utilized for sample amplification efficiency normalization.This approach, however, suffers from several drawbacks. The methodrequires that each sample has equal input amounts of the nucleic acidand that the amplification efficiency between samples is identical untilthe time of analysis. Furthermore, it is difficult using theconventional methods of PCR quantitation such as gel electrophoresis orplate capture hybridization to determine that all samples are in factanalyzed during the log phase of the reaction as required by the method.

Another method called quantitative competitive (QC)-PCR, as the nameimplies, relies on the inclusion of an internal control competitor ineach reaction [Piatak, (1993), BioTechniques]. The efficiency of eachreaction is normalized to the internal competitor. A known amount ofinternal competitor is typically added to each sample. The unknowntarget PCR product is compared with the known competitor PCR product toobtain relative quantitation. A difficulty with this general approachlies in developing an internal control that amplifies with the sameefficiency than the target molecule.

5′Fluorogenic Nuclease Assays

Fluorogenic nuclease assays are a real time quantitation method thatuses a probe to monitor formation of amplification product. The basisfor this method of monitoring the formation of amplification product isto measure continuously PCR product accumulation using a dual-labelledfluorogenic oligonucleotide probe, an approach frequently referred to inthe literature simply as the “TaqMan method” [Piatak,(1993), Science;Heid, (1996); Gibson, (1996); Holland. (1991)].

The probe used in such assays is typically a short (about 20-25 bases)oligonucleotide that is labeled with two different fluorescent dyes. The5′ terminus of the probe is attached to a reporter dye and the 3′terminus is attached to a quenching dye, although the dyes could beattached at other locations on the probe as well. The probe is designedto have at least substantial sequence complementarity with the probebinding site. Upstream and downstream PCR primers which bind to flankingregions of the locus are added to the reaction mixture. When the probeis intact, energy transfer between the two fluorophors occurs and thequencher quenches emission from the reporter. During the extension phaseof PCR, the probe is cleaved by the 5′ nuclease activity of a nucleicacid polymerase such as Taq polymerase, thereby releasing the reporterfrom the oligonucleotide-quencher and resulting in an increase ofreporter emission intensity which can be measured by an appropriatedetector.

One detector which is specifically adapted for measuring fluorescenceemissions such as those created during a fluorogenic assay is the ABI7700 or 4700 HT manufactured by Applied Biosystems, Inc. in Foster City,Calif. The ABI 7700 uses fiber optics connected with each well in a96-or 384 well PCR tube arrangement. The instrument includes a laser forexciting the labels and is capable of measuring the fluorescence spectraintensity from each tube with continuous monitoring during PCRamplification. Each tube is re-examined every 8.5 seconds.

Computer software provided with the instrument is capable of recordingthe fluorescence intensity of reporter and quencher over the course ofthe amplification. The recorded values will then be used to calculatethe increase in normalized reporter emission intensity on a continuousbasis. The increase in emission intensity is plotted versus time, i.e.,the number of amplification cycles, to produce a continuous measure ofamplification. To quantify the locus in each amplification reaction, theamplification plot is examined at a point during the log phase ofproduct accumulation. This is accomplished by assigning a fluorescencethreshold intensity above background and determining the point at whicheach amplification plot crosses the threshold (defined as the thresholdcycle number or Ct). Differences in threshold cycle number are used toquantify the relative amount of PCR target contained within each tube.Assuming that each reaction functions at 100% PCR efficiency, adifference of one Ct represents a two-fold difference in the amount ofstarting template. The fluorescence value can be used in conjunctionwith a standard curve to determine the amount of amplification productpresent.

Non-Probe-Based Detection Methods

A variety of options are available for measuring the amplificationproducts as they are formed. One method utilizes labels, such as dyes,which only bind to double stranded DNA. In this type of approach,amplification product (which is double stranded) binds dye molecules insolution to form a complex. With the appropriate dyes, it is possible todistinguish between dye molecules free in solution and dye moleculesbound to amplification product. For example, certain dyes fluoresce onlywhen bound to amplification product. Examples of dyes which can be usedin methods of this general type include, but are not limited to, SyberGreen.TM. and Pico Green from Molecular Probes, Inc. of Eugene, Oreg.,ethidium bromide, propidium iodide, chromomycin, acridine orange,Hoechst 33258, Toto-1, Yoyo-1, DAPI (4′,6-diamidino-2-phenylindolehydrochloride).

Another real time detection technique measures alteration in energyfluorescence energy transfer between fluorophors conjugated with PCRprimers [Livak, (1995)].

Probe-Based Detection Methods

These detection methods involve some alteration to the structure orconformation of a probe hybridized to the locus between theamplification primer pair. In some instances, the alteration is causedby the template-dependent extension catalyzed by a nucleic acidpolymerase during the amplification process. The alteration generates adetectable signal which is an indirect measure of the amount ofamplification product formed.

For example, some methods involve the degradation or digestion of theprobe during the extension reaction. These methods are a consequence ofthe 5′-3′ nuclease activity associated with some nucleic acidpolymerases. Polymerases having this activity cleave mononucleotides orsmall oligonucleotides from an oligonucleotide probe annealed to itscomplementary sequence located within the locus.

The 3′ end of the upstream primer provides the initial binding site forthe nucleic acid polymerase. As the polymerase catalyzes extension ofthe upstream primer and encounters the bound probe, the nucleic acidpolymerase displaces a portion of the 5′ end of the probe and throughits nuclease activity cleaves mononucleotides or oligonucleotides fromthe probe.

The upstream primer and the probe can be designed such that they annealto the complementary strand in close proximity to one another. In fact,the 3′ end of the upstream primer and the 5′ end of the probe may abutone another. In this situation, extension of the upstream primer is notnecessary in order for the nucleic acid polymerase to begin cleaving theprobe. In the case in which intervening nucleotides separate theupstream primer and the probe, extension of the primer is necessarybefore the nucleic acid polymerase encounters the 5′ end of the probe.Once contact occurs and polymerization continues, the 5′-3′ exonucleaseactivity of the nucleic acid polymerase begins cleaving mononucleotidesor oligonucleotides from the 5′ end of the probe. Digestion of the probecontinues until the remaining portion of the probe dissociates from thecomplementary strand.

In solution, the two end sections can hybridize with each other to forma hairpin loop. In this conformation, the reporter and quencher dye arein sufficiently close proximity that fluorescence from the reporter dyeis effectively quenched by the quencher dye. Hybridized probe, incontrast, results in a linearized conformation in which the extent ofquenching is decreased. Thus, by monitoring emission changes for the twodyes, it is possible to indirectly monitor the formation ofamplification product.

Probes

The labeled probe is selected so that its sequence is substantiallycomplementary to a segment of the test locus or a reference locus. Asindicated above, the nucleic acid site to which the probe binds shouldbe located between the primer binding sites for the upstream anddownstream amplification primers.

Primers

The primers used in the amplification are selected so as to be capableof hybridizing to sequences at flanking regions of the locus beingamplified. The primers are chosen to have at least substantialcomplementarity with the different strands of the nucleic acid beingamplified. When a probe is utilized to detect the formation ofamplification products, the primers are selected in such that they flankthe probe, i.e. are located upstream and downstream of the probe.

The primer must have sufficient length so that it is capable of primingthe synthesis of extension products in the presence of an agent forpolymerization. The length and composition of the primer depends on manyparameters, including, for example, the temperature at which theannealing reaction is conducted, proximity of the probe binding site tothat of the primer, relative concentrations of the primer and probe andthe particular nucleic acid composition of the probe. Typically theprimer includes 15-30 nucleotides. However, the length of the primer maybe more or less depending on the complexity of the primer binding siteand the factors listed above.

Labels for Probes and Primers

The labels used for labeling the probes or primers of the currentinvention and which can provide the signal corresponding to the quantityof amplification product can take a variety of forms. As indicated abovewith regard to the 5′ fluorogenic nuclease method, a fluorescent signalis one signal which can be measured. However, measurements may also bemade, for example, by monitoring radioactivity, colorimetry, absorption,magnetic parameters, or enzymatic activity. Thus, labels which can beemployed include, but are not limited to, fluorophors, chromophores,radioactive isotopes, electron dense reagents, enzymes, and ligandshaving specific binding partners (e.g., biotin-avidin).

Monitoring changes in fluorescence is a particularly useful way tomonitor the accumulation of amplification products. A number of labelsuseful for attachment to probes or primers are commercially availableincluding fluorescein and various fluorescein derivatives such as FAM,HEX, TET and JOE (all which are available from Applied Biosystems,Foster City, Calif.); lucifer yellow, and coumarin derivatives.

Labels may be attached to the probe or primer using a variety oftechniques and can be attached at the 5′ end, and/or the 3′ end and/orat an internal nucleotide. The label can also be attached to spacer armsof various sizes which are attached to the probe or primer. These spacerarms are useful for obtaining a desired distance between multiple labelsattached to the probe or primer.

In some instances, a single label may be utilized; whereas, in otherinstances, such as with the 5′ fluorogenic nuclease assays for example,two or more labels are attached to the probe. In cases wherein the probeincludes multiple labels, it is generally advisable to maintain spacingbetween the labels which is sufficient to permit separation of thelabels during digestion of the probe through the 5′-3′ nuclease activityof the nucleic acid polymerase.

Patients Exhibiting Symptoms of Disease

A number of diseases are associated with changes in the copy number of acertain gene. For patients having symptoms of a disease, the real-timePCR method can be used to determine if the patient has copy numberalterations which are known to be linked with diseases that areassociated with the symptoms the patient has.

5-HT1F Expression

5-HT1F Fusion Proteins

Fusion proteins are useful for generating antibodies against 5-HT1Fpolypeptides and for use in various assay systems. For example, fusionproteins can be used to identify proteins which interact with portionsof 5-HT1F polypeptides. Protein affinity chromatography or library-basedassays for protein-protein interactions, such as the yeast two-hybrid orphage display systems, can be used for this purpose. Such methods arewell known in the art and also can be used as drug screens.

A 5-HT1F fusion protein comprises two polypeptide segments fusedtogether by means of a peptide bond. The first polypeptide segment cancomprise at least 54, 75, 100, 125, 139, 150, 175, 200, 225, 250, or 275contiguous amino acids of SEQ ID NO: 2 or of a biologically activevariant, such as those described above. The first polypeptide segmentalso can comprise full-length 5-HT1F.

The second polypeptide segment can be a full-length protein or a proteinfragment. Proteins commonly used in fusion protein construction include,but are not limited to β galactosidase, β-glucuronidase, greenfluorescent protein (GFP), autofluorescent proteins, including bluefluorescent protein (BFP), glutathione-S-transferase (GST), luciferase,horseradish peroxidase (HRP), and chloramphenicol acetyltransferase(CAT). Additionally, epitope tags are used in fusion proteinconstructions, including histidine (His) tags, FLAG tags, influenzahemagglutinin HA) tags, Myc tags, VSVG tags, and thioredoxin (Trx) tags.Other fusion constructions can include maltose binding protein (MBP),S-tag, Lex a DNA binding domain (DBD) fusions, GAL4 DNA binding domainfusions, herpes simplex virus (ISV) BP16 protein fusions and G-proteinfusions (for example G(alpha)16, Gs, Gi). A fusion protein also can beengineered to contain a cleavage site located adjacent to the 5-HT1F.

Preparation of Polynucleotides

A naturally occurring 5-HT1F polynucleotide can be isolated free ofother cellular components such as membrane components, proteins, andlipids. Polynucleotides can be made by a cell and isolated usingstandard nucleic acid purification techniques, or synthesized using anamplification technique, such as the polymerase chain reaction (PCR), orby using an automatic synthesizer. Methods for isolating polynucleotidesare routine and are known in the art. Any such technique for obtaining apolynucleotide can be used to obtain isolated 5-HT1F polynucleotides.For example, restriction enzymes and probes can be used to isolatepolynucleotide fragments which comprise 5-HT1F nucleotide sequences.Isolated polynucleotides are in preparations which are free or at least70, 80, or 90% free of other molecules.

5-HT1F cDNA molecules can be made with standard molecular biologytechniques, using 5-HT1F mRNA as a template. 5-HT1F cDNA molecules canthereafter be replicated using molecular biology techniques known in theart. An amplification technique, such as PCR, can be used to obtainadditional copies of polynucleotides of the invention, using eitherhuman genomic DNA or cDNA as a template.

Alternatively, synthetic chemistry techniques can be used to synthesizes5-HT1F polynucleotides. The degeneracy of the genetic code allowsalternate nucleotide sequences to be synthesized which will encode5-HT1F having, for example, an amino acid sequence shown in SEQ ID NO: 2or a biologically active variant thereof.

Extending Polynucleotides

Various PCR-based methods can be used to extend nucleic acid sequencesencoding human 5-HT1F, for example to detect upstream sequences of5-HT1F gene such as promoters and regulatory elements. For example,restriction-site PCR uses universal primers to retrieve unknown sequenceadjacent to a known locus. Genomic DNA is first amplified in thepresence of a primer to a linker sequence and a primer specific to theknown region. The amplified sequences are then subjected to a secondround of PCR with the same linker primer and another specific primerinternal to the first one. Products of each round of PCR are transcribedwith an appropriate RNA polymerase and sequenced using reversetranscriptase.

Inverse PCR also can be used to amplify or extend sequences usingdivergent primers based on a known region. Primers can be designed usingcommercially available software, such as OLIGO 4.06 Primer Analysissoftware (National Biosciences Inc., Plymouth, Minn.), to be 22-30nucleotides in length, to have a GC content of 50% or more, and toanneal to the target sequence at temperatures about 68-72° C. The methoduses several restriction enzymes to generate a suitable fragment in theknown region of a gene. The fragment is then circularized byintramolecular ligation and used as a PCR template.

Another method which can be used is capture PCR, which involves PCRamplification of DNA fragments adjacent to a known sequence in human andyeast artificial chromosome DNA. In this method, multiple restrictionenzyme digestions and ligations also can be used to place an engineereddouble-stranded sequence into an unknown fragment of the DNA moleculebefore performing PCR.

When screening for full-length cDNAs, it is preferable to use librariesthat have been size-selected to include larger cDNAs. Randomly-primedlibraries are preferable, in that they will contain more sequences whichcontain the 5′ regions of genes. Use of a randomly primed library may beespecially preferable for situations in which an oligo d(T) library doesnot yield a full-length cDNA. Genomic libraries can be useful forextension of sequence into 5′ non-transcribed regulatory regions.

Commercially available capillary electrophoresis systems can be used toanalyze the size or confirm the nucleotide sequence of PCR or sequencingproducts. For example, capillary sequencing can employ flowable polymersfor electrophoretic separation, four different fluorescent dyes (one foreach nucleotide) which are laser activated, and detection of the emittedwavelengths by a charge coupled device camera. Output/light intensitycan be converted to electrical signal using appropriate equipment andsoftware (e.g., GENOTYPER and Sequence NAVIGATOR, Perkin Elmer), and theentire process from loading of samples to computer analysis andelectronic data display can be computer controlled. Capillaryelectrophoresis is especially preferable for the sequencing of smallpieces of DNA which might be present in limited amounts in a particularsample.

Obtaining Polypeptides

5-HT1F can be obtained, for example, by purification from human cells,by expression of 5-HT1F polynucleotides, or by direct chemicalsynthesis.

Protein Purification

5-HT1F can be purified from any human cell which expresses the receptor,including those which have been transfected with expression constructswhich express 5-HT1F. A purified 5-HT1F is separated from othercompounds which normally associate with S-HT1F in the cell, such ascertain proteins, carbohydrates, or lipids, using methods well-known inthe art. Such methods include, but are not limited to, size exclusionchromatography, ammonium sulfate fractionation, ion exchangechromatography, affinity chromatography, and preparative gelelectrophoresis.

Expression of 5-HT1F Polynucleotides

To express 5-HT1F, 5-HT1F polynucleotides can be inserted into anexpression vector which contains the necessary elements for thetranscription and translation of the inserted coding sequence. Methodswhich are well known to those skilled in the art can be used toconstruct expression vectors containing sequences encoding 5-HT1F andappropriate transcriptional and translational control elements. Thesemethods include in vitro recombinant DNA techniques, synthetictechniques, and in vivo genetic recombination.

A variety of expression vector/host systems can be utilized to containand express sequences encoding 5-HT1F. These include, but are notlimited to, microorganisms, such as bacteria transformed withrecombinant bacteriophage, plasmid, or cosmid DNA expression vectors;yeast transformed with yeast expression vectors, insect cell systemsinfected with virus expression vectors (e.g., baculovirus), plant cellsystems transformed with virus expression vectors (e.g., cauliflowermosaic virus, CaMV; tobacco mosaic virus, TMV) or with bacterialexpression vectors (e.g., Ti or pBR322 plasmids), or animal cellsystems.

The control elements or regulatory sequences are those non-translatedregions of the vector—enhancers, promoters, 5′ and 3′ untranslatedregions—which interact with host cellular proteins to carry outtranscription and translation. Such elements can vary in their strengthand specificity. Depending on the vector system and host utilized, anynumber of suitable transcription and translation elements, includingconstitutive and inducible promoters, can be used. For example, whencloning in bacterial systems, inducible promoters such as the hybridlacZ promoter of the BLUESCRIPT phagemid (Stratagene, LaJolla, Calif.)or pSPORT1 plasmid (Life Technologies) and the like can be used. Thebaculovirus polyhedrin promoter can be used in insect cells. Promotersor enhancers derived from the genomes of plant cells (e.g., heat shock,RUBISCO, and storage protein genes) or from plant viruses (e.g., viralpromoters or leader sequences) can be cloned into the vector. Inmammalian cell systems, promoters from mammalian genes or from mammalianviruses are preferable. If it is necessary to generate a cell line thatcontains multiple copies of a nucleotide sequence encoding 5-HT1F,vectors based on SV40 or EBV can be used with an appropriate selectablemarker.

Bacterial and Yeast Expression Systems

In bacterial systems, a number of expression vectors can be selected.For example, when a large quantity of 5-HT1F is needed for the inductionof antibodies, vectors which direct high level expression of fusionproteins that are readily purified can be used. Such vectors include,but are not limited to, multifunctional E. coli cloning and expressionvectors such as BLUESCRIPT (Stratagene). In a BLUESCRIPT vector, asequence encoding 5-HT1F can be ligated into the vector in frame withsequences for the amino-terminal Met and the subsequent 7 residues ofβ-galactosidase so that a hybrid protein is produced. pIN vectors orpGEX vectors (Promega, Madison, Wis.) also can be used to expressforeign polypeptides as fusion proteins with glutathione S-transferase(GST). In general, such fusion proteins are soluble and can easily bepurified from lysed cells by adsorption to glutathione-agarose beadsfollowed by elution in the presence of free glutathione. Proteins madein such systems can be designed to include heparin, thrombin, or factorXa protease cleavage sites so that the cloned polypeptide of interestcan be released from the GST moiety at will.

Plant and Insect Expression Systems

If plant expression vectors are used, the expression of sequencesencoding 5-HT1F can be driven by any of a number of promoters. Forexample, viral promoters such as the 35S and 19S promoters of CaMV canbe used alone or in combination with the omega leader sequence from TMV.Alternatively, plant promoters such as the small subunit of RUBISCO orheat shock promoters can be used. These constructs can be introducedinto plant cells by direct DNA transformation or by pathogen-mediatedtransfection.

An insect system also can be used to express 5-HT1F. For example, in onesuch system Autographa californica nuclear polyhedrosis virus (AcNPV) isused as a vector to express foreign genes in Spodoptera frugiperda cellsor in Trichoplusia larvae. Sequences encoding 5-HT1F can be cloned intoa non-essential region of the virus, such as the polyhedrin gene, andplaced under control of the polyhedrin promoter. Successful insertion of5-HT1F will render the polyhedrin gene inactive and produce recombinantvirus lacking coat protein. The recombinant viruses can then be used toinfect S. frugiperda cells or Trichoplusia larvae in which 5-HT1F can beexpressed.

Mammalian Expression Systems

A number of viral-based expression systems can be used to express 5-HT1Fin mammalian host cells. For example, if an adenovirus is used as anexpression vector, sequences encoding 5-HT1F can be ligated into anadenovirus transcription/translation complex comprising the latepromoter and tripartite leader sequence. Insertion in a non-essential E1or E3 region of the viral genome can be used to obtain a viable viruswhich is capable of expressing 5-HT1F in infected host cells [Engelhard,1994)]. If desired, transcription enhancers, such as the Rous sarcomavirus (RSV) enhancer, can be used to increase expression in mammalianhost cells.

Human artificial chromosomes (HACs) also can be used to deliver largerfragments of DNA than can be contained and expressed in a plasmid. HACsof 6M to 10M are constructed and delivered to cells via conventionaldelivery methods (e.g., liposomes, polycationic amino polymers, orvesicles). Specific initiation signals also can be used to achieve moreefficient translation of sequences encoding 5-HT1F. Such signals includethe ATG initiation codon and adjacent sequences. In cases wheresequences encoding 5-HT1F, its initiation codon, and upstream sequencesare inserted into the appropriate expression vector, no additionaltranscriptional or translational control signals may be needed. However,in cases where only coding sequence, or a fragment thereof, is inserted,exogenous translational control signals (including the ATG initiationcodon) should be provided. The initiation codon should be in the correctreading frame to ensure translation of the entire insert. Exogenoustranslational elements and initiation codons can be of various origins,both natural and synthetic.

Host Cells

A host cell strain can be chosen for its ability to modulate theexpression of the inserted sequences or to process the expressed 5-HT1Fin the desired fashion. Such modifications of the polypeptide include,but are not limited to, acetylation, carboxylation, glycosylation,phosphorylation, lipidation, and acylation. Post-translationalprocessing which cleaves a “prepro” form of the polypeptide also can beused to facilitate correct insertion, folding and/or function. Differenthost cells which have specific cellular machinery and characteristicmechanisms for post-translational activities (e.g., CHO, HeLa, MDCK,HEK293, and WI38), are available from the American Type CultureCollection (ATCC; 10801 University Boulevard, Manassas, Va. 20110-2209)and can be chosen to ensure the correct modification and processing ofthe foreign protein.

Stable expression is preferred for long-term, high-yield production ofrecombinant proteins. For example, cell lines which stably express5-HT1F can be transformed using expression vectors which can containviral origins of replication and/or endogenous expression elements and aselectable marker gene on the same or on a separate vector. Followingthe introduction of the vector, cells can be allowed to grow for 1-2days in an enriched medium before they are switched to a selectivemedium. The purpose of the selectable marker is to confer resistance toselection, and its presence allows growth and recovery of cells whichsuccessfully express the introduced 5-HT1F sequences. Resistant clonesof stably transformed cells can be proliferated using tissue culturetechniques appropriate to the cell type. Any number of selection systemscan be used to recover transformed cell lines. These include, but arenot limited to, the herpes simplex virus thymidine kinase [Logan,(1984)] and adenine phosphoribosyltransferase [Wigler, (1977)] geneswhich can be employed in tk⁻ or aprf cells, respectively. Also,antimetabolite, antibiotic, or herbicide resistance can be used as thebasis for selection. For example, dhfr confers resistance tomethotrexate [Lowy, (1980)], npt confers resistance to theaminoglycosides, neomycin and G-418 [Wigler, (1980)], and als and patconfer resistance to chlorsulfuron and phosphinotricinacetyltransferase, respectively [Colbere-Garapin, 1981]. Additionalselectable genes have been described. For example, trpB allows cells toutilize indole in place of tryptophan, or hisD, which allows cells toutilize histinol in place of histidine. Visible markers such asanthocyanins, β-glucuronidase and its substrate GUS, and luciferase andits substrate luciferin, can be used to identify transformants and toquantify the amount of transient or stable protein expressionattributable to a specific vector system

Detecting Polypeptide Expression

Although the presence of marker gene expression suggests that a 5-HT1Fpolynucleotide is also present, its presence and expression may need tobe confirmed. For example, if a sequence encoding 5-HT1F is insertedwithin a marker gene sequence, transformed cells containing sequenceswhich encode 5-HT1F can be identified by the absence of marker genefunction. Alternatively, a marker gene can be placed in tandem with asequence encoding 5-HT1F under the control of a single promoter.Expression of the marker gene in response to induction or selectionusually indicates expression of 5-HT1F polynucleotide.

Alternatively, host cells which contain a 5-HT1F polynucleotide andwhich express 5-HT1F can be identified by a variety of procedures knownto those of skill in the art. These procedures include, but are notlimited to, DNA-DNA or DNA-RNA hybridizations and protein bioassay orimmunoassay techniques which include membrane, solution, or chip-basedtechnologies for the detection and/or quantification of nucleic acid orprotein. For example, the presence of a polynucleotide sequence encoding5-HT1F can be detected by DNA-DNA or DNA-RNA hybridization oramplification using probes or fragments or fragments of polynucleotidesencoding 5-HT1F. Nucleic acid amplification-based assays involve the useof oligonucleotides selected from sequences encoding 5-HT1F to detecttransformants which contain a 5-HT1F polynucleotide.

A variety of protocols for detecting and measuring the expression of5-HT1F, using either polyclonal or monoclonal antibodies specific forthe polypeptide, are known in the art. Examples include enzyme-linkedimmunosorbent assay (ELISA), radioimmunoassay (RIA), and fluorescenceactivated cell sorting (FACS). A two-site, monoclonal-based immunoassayusing monoclonal antibodies reactive to two non-interfering epitopes on5-HT1F can be used, or a competitive binding assay can be employed.

A wide variety of labels and conjugation techniques are known by thoseskilled in the art and can be used in various nucleic acid and aminoacid assays. Means for producing labeled hybridization or PCR probes fordetecting sequences related to polynucleotides encoding 5-HT1F includeoligolabeling, nick translation, end-labeling, or PCR amplificationusing a labeled nucleotide. Alternatively, sequences encoding 5-HT1F canbe cloned into a vector for the production of an mRNA probe. Suchvectors are known in the art, are commercially available, and can beused to synthesize RNA probes in vitro by addition of labelednucleotides and an appropriate RNA polymerase such as T7, T3, or SP6.These procedures can be conducted using a variety of commerciallyavailable kits (Amersham Pharmacia Biotech, Promega, and USBiochemical). Suitable reporter molecules or labels which can be usedfor ease of detection include radionuclides, enzymes, and fluorescent,chemiluminescent, or chromogenic agents, as well as substrates,cofactors, inhibitors, magnetic particles, and the like.

Expression and Purification of Polypeptides

Host cells transformed with 5-HT1F polynucleotides can be cultured underconditions suitable for the expression and recovery of the protein fromcell culture. The polypeptide produced by a transformed cell can besecreted or contained intracellularly depending on the sequence and/orthe vector used. As will be understood by those of skill in the art,expression vectors containing 5-HT1F polynucleotides can be designed tocontain signal sequences which direct secretion of soluble 5-HT1Fthrough a prokaryotic or eukaryotic cell membrane or which direct themembrane insertion of membrane-bound 5-HT1F.

As discussed above, other constructions can be used to join a sequenceencoding 5-HT1F to a nucleotide sequence encoding a polypeptide domainwhich will facilitate purification of soluble proteins. Suchpurification facilitating domains include, but are not limited to, metalchelating peptides such as histidine-tryptophan modules that allowpurification on immobilized metals, protein A domains that allowpurification on immobilized immunoglobulin, and the domain utilized inthe FLAGS extension/affinity purification system (Immunex Corp.,Seattle, Wash.). Inclusion of cleavable linker sequences such as thosespecific for Factor XA or enterokinase nitrogen, San Diego, Calif.)between the purification domain and 5-HT1F also can be used tofacilitate purification. One such expression vector provides forexpression of a fusion protein containing 5-HT1F and 6 histidineresidues preceding a thioredoxin or an enterokinase cleavage site. Thehistidine residues facilitate purification by IMAC (immobilized metalion affinity chromatography) Maddox, (1983)], while the enterokinasecleavage site provides a means for purifying 5-HT1F from the fusionprotein [Porath, (1992)].

Chemical Synthesis

Sequences encoding 5-HT1F can be synthesized, in whole or in part, usingchemical methods well known in the art. Alternatively, 5-HT1F itself canbe produced using chemical methods to synthesize its amino acidsequence, such as by direct peptide synthesis using solid-phasetechniques. Protein synthesis can either be performed using manualtechniques or by automation. Automated synthesis can be achieved, forexample, using Applied Biosystems 431A Peptide Synthesizer (PerkinElmer). Optionally, fragments of 5-HT1F can be separately synthesizedand combined using chemical methods to produce a full-length molecule.

The newly synthesized peptide can be substantially purified bypreparative high performance liquid chromatography. The composition of asynthetic 5-HT1F can be confirmed by amino acid analysis or sequencing.Additionally, any portion of the amino acid sequence of 5-HT1F can bealtered during direct synthesis and/or combined using chemical methodswith sequences from other proteins to produce a variant polypeptide or afusion protein.

Production of Altered Polypeptides

As will be understood by those of skill in the art, it-may beadvantageous to produce 5-HT1F polynucleotides possessing non-naturallyoccurring codons. For example, codons preferred by a particularprokaryotic or eukaryotic host can be selected to increase the rate ofprotein expression or to produce an RNA transcript having desirableproperties, such as a half-life which is longer than that of atranscript generated from the naturally occurring sequence.

The nucleotide sequences referred to herein can be engineered usingmethods generally known in the art to alter 5-HT1F polynucleotides for avariety of reasons, including but not limited to, alterations whichmodify the cloning, processing, and/or expression of the polypeptide ormRNA product. DNA shuffling by random fragmentation and PCR reassemblyof gene fragments and synthetic oligonucleotides can be used to engineerthe nucleotide sequences. For example, site-directed mutagenesis can beused to insert new restriction sites, alter glycosylation patterns,change codon preference, produce splice variants, introduce mutations,and so forth.

Antibodies

Any type of antibody known in the art can be generated to bindspecifically to an epitope of 5-HT1F.

“Antibody” as used herein includes intact immunoglobulin molecules, aswell as fragments thereof, such as Fab, F(ab′)₂, and Fv, which arecapable of binding an epitope of 5-HT1F. Typically, at least 6, 8, 10,or 12 contiguous amino acids are required to form an epitope. However,epitopes which involve non-contiguous amino acids may require more,e.g., at least 15, 25, or 50 amino acid. An antibody which specificallybinds to an epitope of 5-HT1F can be used therapeutically, as well as inimmunochemical assays, such as Western blots, ELISAs, radioimmunoassays,immunohistochemical assays, immunoprecipitations, or otherimmunochemical assays known in the art. Various immunoassays can be usedto identify antibodies having the desired specificity. Numerousprotocols for competitive binding or immunoradiometric assays are wellknown in the art. Such immunoassays typically involve the measurement ofcomplex formation between an immunogen and an antibody whichspecifically binds to the 5-HT1F immunogen.

Typically, an antibody which specifically binds to 5-HT1F provides adetection signal at least 5-, 10-, or 20-fold higher than a detectionsignal provided with other proteins when used in an immunochemicalassay. Preferably, antibodies which specifically bind to 5-HT1F do notdetect other proteins in immunochemical assays and can immunoprecipitate5-HT1F from solution.

5-HT1F can be used to immunize a mammal, such as a mouse, rat, rabbit,guinea pig, monkey, or human, to produce polyclonal antibodies. Ifdesired, 5-HT1F can be conjugated to a carrier protein, such as bovineserum albumin, thyroglobulin, and keyhole limpet hemocyanin. Dependingon the host species, various adjuvants can be used to increase theimmunological response. Such adjuvants include, but are not limited to,Freund's adjuvant, mineral gels (e.g., aluminum hydroxide), and surfaceactive substances (e.g., lysolecithin, pluronic polyols, polyanions,peptides, oil emulsions, keyhole limpet hemocyanin, and dinitrophenol).Among adjuvants used in humans, BCG (bacilli Calmette-Guerin) andCorynebacterium parvum are especially useful.

Monoclonal antibodies which specifically bind to 5-HT1F can be preparedusing any technique which provides for the production of antibodymolecules by continuous cell lines in culture. These techniques include,but are not limited to, the hybridoma technique, the human B-cellhybridoma technique, and the EBV-hybridoma technique [Roberge, (1995)].

In addition, techniques developed for the production of “chimericantibodies”, the splicing of mouse antibody genes to human antibodygenes to obtain a molecule with appropriate antigen specificity andbiological activity, can be used. Monoclonal and other antibodies alsocan be “humanized” to prevent a patient from mounting an immune responseagainst the antibody when it is used therapeutically. Such antibodiesmay be sufficiently similar in sequence to human antibodies to be useddirectly in therapy or may require alteration of a few key residues.Sequence differences between rodent antibodies and human sequences canbe minimized by replacing residues which differ from those in the humansequences by site directed mutagenesis of individual residues or bygrating of entire complementarity determining regions. Antibodies whichspecifically bind to 5-HT1F can contain antigen binding sites which areeither partially or fully humanized, as disclosed in U.S. Pat. No.5,565,332.

Alternatively, techniques described for the production of single chainantibodies can be adapted using methods known in the art to producesingle chain antibodies which specifically bind to 5-HT1F. Antibodieswith related specificity, but of distinct idiotypic composition, can begenerated by chain shuffling from random combinatorial immunoglobinlibraries. Single-chain antibodies also can be constructed using a DNAamplification method, such as PCR, using hybridoma cDNA as a template.Single-chain antibodies can be mono- or bispecific, and can be bivalentor tetravalent. Construction of tetravalent, bispecific single-chainantibodies is taught. A nucleotide sequence encoding a single-chainantibody can be constructed using manual or automated nucleotidesynthesis, cloned into an expression construct using standardrecombinant DNA methods, and introduced into a cell to express thecoding sequence, as described below. Alternatively, single-chainantibodies can be produced directly using, for example, filamentousphage technology.

Antibodies which specifically bind to 5-HT1F also can be produced byinducing in vivo production in the lymphocyte population or by screeningimmunoglobulin libraries or panels of highly specific binding reagents.Other types of antibodies can be constructed and used therapeutically inmethods of the invention. For example, chimeric antibodies can beconstructed as disclosed in WO 93/03151. Binding proteins which arederived from immunoglobulins and which are multivalent andmultispecific, such as the “diabodies” described in WO 94/13804, alsocan be prepared.

Antibodies according to the invention can be purified by methods wellknown in the art. For example, antibodies can be affinity purified bypassage over a column to which 5-HT1F is bound. The bound antibodies canthen be eluted from the column using a buffer with a high saltconcentration.

Antisense Oligonucleotides

Antisense oligonucleotides are nucleotide sequences which arecomplementary to a specific DNA or RNA sequence. Once introduced into acell, the complementary nucleotides combine with natural sequencesproduced by the cell to form complexes and block either transcription ortranslation. Preferably, an antisense oligonucleotide is at least 11nucleotides in length, but can be at least 12, 15, 20, 25, 30, 35, 40,45, or 50 or more nucleotides long. Longer sequences also can be used.Antisense oligonucleotide molecules can be provided in a DNA constructand introduced into a cell as described above to decrease the level of5-HT1F gene products in the cell.

Antisense oligonucleotides can be deoxyribonucleotides, ribonucleotides,or a combination of both. Oligonucleotides can be synthesized manuallyor by an automated synthesizer, by covalently linking the 5′ end of onenucleotide with the 3′ end of another nucleotide with non-phosphodiesterinternucleotide linkages such alkylphosphonates, phosphorothioates,phosphorodithioates, alkylphosphonothioates, alkylphosphonates,phosphoramidates, phosphate esters, carbamates, acetamidate,carboxymethyl esters, carbonates, and phosphate triesters.

Modifications of 5-HT1F gene expression can be obtained by designingantisense oligonucleotides which will form duplexes to the control, 5′,or regulatory regions of the 5-HT1F gene. Oligonucleotides derived fromthe transcription initiation site, e.g., between positions −10 and +10from the start site, are preferred. Similarly, inhibition can beachieved using “triple helix” base-pairing methodology. Triple helixpairing is useful because it causes inhibition of the ability of thedouble helix to open sufficiently for the binding of polymerases,transcription factors, or chaperons. Therapeutic advances using triplexDNA have been described in the literature [Nicholls, (1993)]. Anantisense oligonucleotide also can be designed to block translation ofmRNA by preventing the transcript from binding to ribosomes.

Precise complementarity is not required for successful complex formationbetween an antisense oligonucleotide and the complementary sequence of a5-HT1F polynucleotide. Antisense oligonucleotides which comprise, forexample, 2, 3, 4, or 5 or more stretches of contiguous nucleotides whichare precisely complementary to a 5-HT1F polynucleotide, each separatedby a stretch of contiguous nucleotides which are not complementary toadjacent 5-HT1F nucleotides, can provide sufficient targetingspecificity for 5-HT1F mRNA. Preferably, each stretch of complementarycontiguous nucleotides is at least 4, 5, 6, 7, or 8 or more nucleotidesin length. Noncomplementary intervening sequences are preferably 1, 2,3, or 4 nucleotides in length. One skilled in the art can easily use thecalculated melting point of an antisense-sense pair to determine thedegree of mismatching which will be tolerated between a particularantisense oligonucleotide and a particular 5-HT1F polynucleotidesequence. Antisense oligonucleotides can be modified without affectingtheir ability to hybridize to a 5-HT1F polynucleotide. Thesemodifications can be internal or at one or both ends of the antisensemolecule. For example, internucleoside phosphate linkages can bemodified by adding cholesteryl or diamine moieties with varying numbersof carbon residues between the amino groups and terminal ribose.Modified bases and/or sugars, such as arabinose instead of ribose, or a3′,5′-substituted oligonucleotide in which the 3′ hydroxyl group or the5′ phosphate group are substituted, also can be employed in a modifiedantisense oligonucleotide. These modified oligonucleotides can beprepared by methods well known in the art.

Ribozymes

Ribozymes, are RNA molecules with catalytic activity [Uhlmann, (1987)].Ribozymes can be used to inhibit gene function by cleaving an RNAsequence, as is known in the art. The mechanism of ribozyme actioninvolves sequence-specific hybridization of the ribozyme molecule tocomplementary target RNA, followed by endonucleolytic cleavage. Examplesinclude engineered hammerhead motif ribozyme molecules that canspecifically and efficiently catalyze endonucleolytic cleavage ofspecific nucleotide sequences. The coding sequence of a 5-HT1Fpolynucleotide can be used to generate ribozymes which will specificallybind to mRNA transcribed from a 5-HT1F polynucleotide. Methods ofdesigning and constructing ribozymes which can cleave other RNAmolecules in trans in a highly sequence specific manner have beendeveloped and described in the art. For example, the cleavage activityof ribozymes can be targeted to specific RNAs by engineering a discrete“hybridization” region into the ribozyme. The hybridization regioncontains a sequence complementary to the target RNA and thusspecifically hybridizes with the target RNA.

Specific ribozyme cleavage sites within a 5-HT1F RNA target can beidentified by scanning the target molecule for ribozyme cleavage siteswhich include the following sequences: GUA, GUU, and GUC. Onceidentified, short RNA sequences of between 15 and 20 ribonucleotidescorresponding to the region of the target RNA containing the cleavagesite can be evaluated for secondary structural features which may renderthe target inoperable. Suitability of candidate 5-HT1F RNA targets alsocan be evaluated by testing accessibility to hybridization withcomplementary oligonucleotides using ribonuclease protection assays. Thenucleotide sequences shown in SEQ ID NO: 1 and its complement providesources of suitable hybridization region sequences. Longer complementarysequences can be used to increase the affinity of the hybridizationsequence for the target. The hybridizing and cleavage regions of theribozyme can be integrally related such that upon hybridizing to thetarget RNA through the complementary regions, the catalytic region ofthe ribozyme can cleave the target.

Ribozymes can be introduced into cells as part of a DNA construct.Mechanical methods, such as microinjection, liposome-mediatedtransfection, electroporation, or calcium phosphate precipitation, canbe used to introduce a ribozyme-containing DNA construct into cells inwhich it is desired to decrease 5-HT1F expression. Alternatively, if itis desired that the cells stably retain the DNA construct, the constructcan be supplied on a plasmid and maintained as a separate element orintegrated into the genome of the cells, as is known in the art. Aribozyme-encoding DNA construct can include transcriptional regulatoryelements, such as a promoter element, an enhancer or UAS element, and atranscriptional terminator signal, for controlling transcription ofribozymes in the cells (U.S. Pat. No. 5,641,673). Ribozymes also can beengineered to provide an additional level of regulation, so thatdestruction of mRNA occurs only when both a ribozyme and a target geneare induced in the cells.

Screening/Screening Assays

Regulators

Regulators as used herein, refer to compounds that affect the activityof a 5-HT1F in vivo and/or in vivo. Regulators can be agonists andantagonists of a 5-HT1F polypeptide and can be compounds that exerttheir effect on the 5-HT1F activity via the expression, viapost-translational modifications or by other means. Agonists of 5-HT1Fare molecules which, when bound to 5-HT1F, increase or prolong theactivity of S-HT1F. Agonists of 5-HT1F include proteins, nucleic acids,carbohydrates, small molecules, or any other molecule which activate5-HT1F. Antagonists of 5-HT1F are molecules which, when bound to 5-HT1F,decrease the amount or the duration of the activity of 5-HT1F.Antagonists include proteins, nucleic acids, carbohydrates, antibodies,small molecules, or any other molecule which decrease the activity of5-HT1F.

The term “modulate”, as it appears herein, refers to a change in theactivity of 5-HT1F polypeptide. For example, modulation may cause anincrease or a decrease in protein activity, binding characteristics, orany other biological, functional, or immunological properties of 5-HT1F.

As used herein, the terms “specific binding” or “specifically binding”refer to that interaction between a protein or peptide and an agonist,an antibody, or an antagonist. The interaction is dependent upon thepresence of a particular structure of the protein recognized by thebinding molecule (i.e., the antigenic determinant or epitope). Forexample, if an antibody is specific for epitope “A” the presence of apolypeptide containing the epitope A, or the presence of free unlabeledA, in a reaction containing free labeled A and the antibody will reducethe amount of labeled A that binds to the antibody.

The invention provides methods (also referred to herein as “screeningassays”) for identifying compounds which can be used for the treatmentof hematological and cardiovascular diseases, disorders of theperipheral and central nervous system, COPD, asthma, genito-urologicaldisorders and inflammation diseases. The methods entail theidentification of candidate or test compounds or agents (e.g., peptides,peptidomimetics, small molecules or other molecules) which bind to5-HT1F and/or have a stimulatory or inhibitory effect on the biologicalactivity of 5-HT1F or its expression and then determining which of thesecompounds have an effect on symptoms or diseases regarding thehematological and cardiovascular diseases, disorders of the peripheraland central nervous system, COPD, asthma, genito-urological disordersand inflammation diseases in an in vivo assay.

Candidate or test compounds or agents which bind to 5-HT1F and/or have astimulatory or inhibitory effect on the activity or the expression of5-HT1F are identified either in assays that employ cells which express5-HT1F on the cell surface (cell-based assays) or in assays withisolated 5-HT1F (cell-free assays). The various assays can employ avariety of variants of 5-HT1F (e.g., full-length 5-HT1F, a biologicallyactive fragment of 5-HT1F, or a fusion protein which includes all or aportion of 5-HT1F). Moreover, 5-HT1F can be derived from any suitablemammalian species (e.g., human 5-HT1F, rat 5-HT1F or murine 5-HT1F). Theassay can be a binding assay entailing direct or indirect measurement ofthe binding of a test compound or a known 5-HT1F ligand to 5-HT1F. Theassay can also be an activity assay entailing direct or indirectmeasurement of the activity of 5-HT1F. The assay can also be anexpression assay entailing direct or indirect measurement of theexpression of 5-HT1F mRNA or 5-HT1F protein. The various screeningassays are combined with an in vivo assay entailing measuring the effectof the test compound on the symptoms of hematological and cardiovasculardiseases, disorders of the peripheral and central nervous system, COPD,asthma, genito-urological disorders and inflammation diseases.

In one embodiment, the invention provides assays for screening candidateor test compounds which bind to or modulate the activity of amembrane-bound (cell surface expressed) form of 5-HT1F. Such assays canemploy full-length 5-HT1F, a biologically active fragment of 5-HT1F, ora fusion protein which includes all or a portion of 5-HT1F. As describedin greater detail below, the test compound can be obtained by anysuitable means, e.g., from conventional compound libraries. Determiningthe ability of the test compound to bind to a membrane-bound form of5-HT1F can be accomplished, for example, by coupling the test compoundwith a radioisotope or enzymatic label such that binding of the testcompound to the 5-HT1F expressing cell can be measured by detecting thelabeled compound in a complex. For example, the test compound can belabelled with ¹²⁵I, ³⁵S, ¹⁴C, or ³H, either directly or indirectly, andthe radioisotope detected by direct counting of radioemmission or byscintillation counting. Alternatively, the test compound can beenzymatically labelled with, for example, horseradish peroxidase,alkaline phosphatase, or luciferase, and the enzymatic label detected bydetermination of conversion of an appropriate substrate to product.

In a competitive binding format, the assay comprises contacting 5-HT1Fexpressing cell with a known compound which binds to 5-HT1F to form anassay mixture, contacting the assay mixture with a test compound, anddetermining the ability of the test compound to interact with the 5-HT1Fexpressing cell, wherein determining the ability of the test compound tointeract with the 5-HT1F expressing cell comprises determining theability of the test compound to preferentially bind the 5-HT1Fexpressing cell as compared to the known compound.

In another embodiment, the assay is a cell-based assay comprisingcontacting a cell expressing a membrane-bound form of 5-HT1F (e.g.,full-length 5-HT1F, a biologically active fragment of 5-HT1F, or afusion protein which includes all or a portion of 5-HT1F) expressed onthe cell surface with a test compound and determining the ability of thetest compound to modulate (e.g., stimulate or inhibit) the activity ofthe membrane-bound form of 5-HT1F. Determining the ability of the testcompound to modulate the activity of the membrane-bound form of 5-HT1Fcan be accomplished by any method suitable for measuring the activity of5-HT1F, e.g., any method suitable for measuring the activity of aG-protein coupled receptor or other seven-transmembrane receptor(described in greater detail below). The activity of aseven-transmembrane receptor can be measured in a number of ways, notall of which are suitable for any given receptor. Among the measures ofactivity are: alteration in intracellular Ca²⁺ concentration, activationof phospholipase C, alteration in intracellular inositol triphosphate(IP₃) concentration, alteration in intracellular diacylglycerol (DAG)concentration, and alteration in intracellular adenosine cyclic3′,5′-monophosphate (cAMP) concentration.

Determining the ability of the test compound to modulate the activity of5-HT1F can be accomplished, for example, by determining the ability of5-HT1F to bind to or interact with a target molecule. The targetmolecule can be a molecule with which 5-HT1F binds or interacts with innature, for example, a molecule on the surface of a cell which expresses5-HT1F, a molecule on the surface of a second cell, a molecule in theextracellular milieu, a molecule associated with the internal surface ofa cell membrane or a cytoplasmic molecule. The target molecule can be acomponent of a signal transduction pathway which facilitatestransduction of an extracellular signal (e.g., a signal generated bybinding of a 5-HT1F ligand, through the cell membrane and into the cell.The target 5-HT1F molecule can be, for example, a second intracellularprotein which has catalytic activity or a protein which facilitates theassociation of downstream signaling molecules with 5-HT1F.

Determining the ability of 5-HT1F to bind to or interact with a targetmolecule can be accomplished by one of the methods described above fordetermining direct binding. In one embodiment, determining the abilityof a polypeptide of the invention to bind to or interact with a targetmolecule can be accomplished by determining the activity of the targetmolecule. For example, the activity of the target molecule can bedetermined by detecting induction of a cellular second messenger of thetarget (e.g., intracellular Ca²⁺, diacylglycerol, IP₃, etc.), detectingcatalytic/enzymatic activity of the target on an appropriate substrate,detecting the induction of a reporter gene (e.g., a regulatory elementthat is responsive to a polypeptide of the invention operably linked toa nucleic acid encoding a detectable marker, e.g., luciferase), ordetecting a cellular response.

The present invention also includes cell-free assays. Such assaysinvolve contacting a form of 5-HT1F (e.g., full-length 5-HT1F, abiologically active fragment of 5-HT1F, or a fusion protein comprisingall or a portion of 5-HT1F) with a test compound and determining theability of the test compound to bind to 5-HT1F. Binding of the testcompound to 5-HT1F can be determined either directly or indirectly asdescribed above. In one embodiment, the assay includes contacting 5-HT1Fwith a known compound which binds 5-HT1F to form an assay mixture,contacting the assay mixture with a test compound, and determining theability of the test compound to interact with 5-HT1F, whereindetermining the ability of the test compound to interact with 5-HT1Fcomprises determining the ability of the test compound to preferentiallybind to 5-HT1F as compared to the known compound.

The cell-free assays of the present invention are amenable to use ofeither a membrane-bound form of 5-HT1F or a soluble fragment thereof. Inthe case of cell-free assays comprising the membrane-bound form of thepolypeptide, it may be desirable to utilize a solubilizing agent suchthat the membrane-bound form of the polypeptide is maintained insolution. Examples of such solubilizing agents include but are notlimited to non-ionic detergents such as n-octylglucoside,n-dodecylglucoside, n-dodecylmaltoside, octanoyl-N-methylglucamide,decanoyl-N-methylglucamide, Triton X-100, Triton X-114, Thesit,Isotridecypoly(ethylene glycol ether)n,3-[(3-cholamidopropyl)dimethylamminio]-1-propane sulfonate (CHAPS),3-[(3-cholamidopropyl)dimethylamminio]-2-hydroxy-1-propane sulfonate(CHAPSO), or N-dodecyl=N,N-dimethyl-3-ammonio-1-propane sulfonate.

In various embodiments of the above assay methods of the presentinvention, it may be desirable to immobilize 5-HT1F (or a 5-HT1F targetmolecule) to facilitate separation of complexed from uncomplexed formsof one or both of the proteins, as well as to accommodate automation ofthe assay. Binding of a test compound to 5-HT1F, or interaction of5-HT1F with a target molecule in the presence and absence of a candidatecompound, can be accomplished in any vessel suitable for containing thereactants. Examples of such vessels include microtitre plates, testtubes, and microcentrifuge tubes. In one embodiment, a fusion proteincan be provided which adds a domain that allows one or both of theproteins to be bound to a matrix. For example, glutathione-S-transferase(GST) fusion proteins or glutathione-S-transferase fusion proteins canbe adsorbed onto glutathione sepharose beads (Sigma Chemical; St. Louis,Mo.) or glutathione derivatized microtitre plates, which are thencombined with the test compound or the test compound and either thenon-adsorbed target protein or 5-HT1F, and the mixture incubated underconditions conducive to complex formation (e.g., at physiologicalconditions for salt and pH). Following incubation, the beads ormicrotitre plate wells are washed to remove any unbound components andcomplex formation is measured either directly or indirectly, forexample, as described above. Alternatively, the complexes can bedissociated from the matrix, and the level of binding or activity of5-HT1F can be determined using standard techniques.

Other techniques for immobilizing proteins on matrices can also be usedin the screening assays of the invention. For example, either 5-HT1F orits target molecule can be immobilized utilizing conjugation of biotinand streptavidin. Biotinylated polypeptide of the invention or targetmolecules can be prepared from biotin-NHS (N-hydroxy-succinimide) usingtechniques well known in the art (e.g., biotinylation kit, PierceChemicals; Rockford, Ill.), and immobilized in the wells ofstreptavidin-coated plates Pierce Chemical). Alternatively, antibodiesreactive with 5-HT1F or target molecules but which do not interfere withbinding of the polypeptide of the invention to its target molecule canbe derivatized to the wells of the plate, and unbound target orpolypeptide of the invention trapped in the wells by antibodyconjugation. Methods for detecting such complexes, in addition to thosedescribed above for the GST-immobilized complexes, includeimmunodetection of complexes using antibodies reactive with 5-HT1F ortarget molecule, as well as enzyme-linked assays which rely on detectingan enzymatic activity associated with 5-HT1F or target molecule.

The screening assay can also involve monitoring the expression of5-HT1F. For example, regulators of expression of 5-HT1F can beidentified in a method in which a cell is contacted with a candidatecompound and the expression of 5-HT1F protein or mRNA in the cell isdetermined. The level of expression of 5-HT1F protein or mRNA thepresence of the candidate compound is compared to the level ofexpression of 5-HT1F protein or mRNA in the absence of the candidatecompound. The candidate compound can then be identified as a regulatorof expression of 5-HT1F based on this comparison. For example, whenexpression of 5-HT1F protein or mRNA protein is greater (statisticallysignificantly greater) in the presence of the candidate compound than inits absence, the candidate compound is identified as a stimulator of5-HT1F protein or mRNA expression. Alternatively, when expression of5-HT1F protein or mRNA is less (statistically significantly less) in thepresence of the candidate compound than in its absence, the candidatecompound is identified as an inhibitor of 5-HT1F protein or mRNAexpression. The level of 5-HT1F protein or mRNA expression in the cellscan be determined by methods described below.

Binding Assays

For binding assays, the test compound is preferably a small moleculewhich binds to and occupies the active site of 5-HT1F polypeptide,thereby making the ligand binding site inaccessible to substrate suchthat normal biological activity is prevented. Examples of such smallmolecules include, but are not limited to, small peptides orpeptide-like molecules. Potential ligands which bind to a polypeptide ofthe invention include, but are not limited to, the natural ligands ofknown 5-HT1F GPCRs and analogues or derivatives thereof.

In binding assays, either the test compound or the 5-HT1F polypeptidecan comprise a detectable label, such as a fluorescent, radioisotopic,chemiluminescent, or enzymatic label, such as horseradish peroxidase,alkaline phosphatase, or luciferase. Detection of a test compound whichis bound to 5-HT1F polypeptide can then be accomplished, for example, bydirect counting of radioemmission, by scintillation counting, or bydetermining conversion of an appropriate substrate to a detectableproduct. Alternatively, binding of a test compound to a 5-HT1Fpolypeptide can be determined without labeling either of theinteractants. For example, a microphysiometer can be used to detectbinding of a test compound with a 5-HT1F polypeptide. A microphysiometer(e.g., Cytosensor™) is an analytical instrument that measures the rateat which a cell acidifies its environment using a light-addressablepotentiometric sensor (LAPS). Changes in this acidification rate can beused as an indicator of the interaction between a test compound and5-HT1F [Haseloff, (1988)].

Determining the ability of a test compound to bind to 5-HT1F also can beaccomplished using a technology such as real-time BimolecularInteraction Analysis (BIA) [McConnell, (1992); Sjolander, (1991)]. BIAis a technology for studying biospecific interactions in real time,without labeling any of the interactants (e.g., BIAcore™). Changes inthe optical phenomenon surface plasmon resonance (SPR) can be used as anindication of real-time reactions between biological molecules.

In yet another aspect of the invention, a 5-HT1F-like polypeptide can beused as a “bait protein” in a two-hybrid assay or three-hybrid assay[Szabo, (1995); U.S. Pat. No. 5,283,317), to identify other proteinswhich bind to or interact with 5-HT1F and modulate its activity.

The two-hybrid system is based on the modular nature of mosttranscription factors, which consist of separable DNA-binding andactivation domains. Briefly, the assay utilizes two different DNAconstructs. For example, in one construct, polynucleotide encoding5-HT1F can be fused to a polynucleotide encoding the DNA binding domainof a known transcription factor (e.g., GAL-4). In the other construct aDNA sequence that encodes an unidentified protein (“prey” or “sample”)can be fused to a polynucleotide that codes for the activation domain ofthe known transcription factor. If the “bait” and the “prey” proteinsare able to interact in vivo to form an protein-dependent complex, theDNA-binding and activation domains of the transcription factor arebrought into close proximity. This proximity allows transcription of areporter gene (e.g., LacZ), which is operably linked to atranscriptional regulatory site responsive to the transcription factor.Expression of the reporter gene can be detected, and cell coloniescontaining the functional transcription factor can be isolated and usedto obtain the DNA sequence encoding the protein which interacts with5-HT1F.

It may be desirable to immobilize either the 5-HT1F (or polynucleotide)or the test compound to facilitate separation of the bound form fromunbound forms of one or both of the interactants, as well as toaccommodate automation of the assay. Thus, either the 5-HT1F-likepolypeptide (or polynucleotide) or the test compound can be bound to asolid support. Suitable solid supports include, but are not limited to,glass or plastic slides, tissue culture plates, microtiter wells, tubes,silicon chips, or particles such as beads (including, but not limitedto, latex, polystyrene, or glass beads). Any method known in the art canbe used to attach 5-HT1F-like polypeptide (or polynucleotide) or testcompound to a solid support, including use of covalent and non-covalentlinkages, passive absorption, or pairs of binding moieties attachedrespectively to the polypeptide (or polynucleotide) or test compound andthe solid support. Test compounds are preferably bound to the solidsupport in an array, so that the location of individual test compoundscan be tracked. Binding of a test compound to 5-HT1F (or apolynucleotide encoding for 5-HT1F) can be accomplished in any vesselsuitable for containing the reactants. Examples of such vessels includemicrotiter plates, test tubes, and microcentrifuge tubes.

In one embodiment, 5-HT1F is a fusion protein comprising a domain thatallows binding of 5-HT1F to a solid support. For example,glutathione-S-transferase fusion proteins can be adsorbed ontoglutathione sepharose beads (Sigma Chemical, St. Louis, Mo.) orglutathione derivatized microtiter plates, which are then combined withthe test compound or the test compound and the non-adsorbed 5-HT1F; themixture is then incubated under conditions conducive to complexformation (e.g., at physiological conditions for salt and pH). Followingincubation, the beads or microtiter plate wells are washed to remove anyunbound components. Binding of the interactants can be determined eitherdirectly or indirectly, as described above. Alternatively, the complexescan be dissociated from the solid support before binding is determined.

Other techniques for immobilizing proteins or polynucleotides on a solidsupport also can be used in the screening assays of the invention. Forexample, either 5-HT1F (or a polynucleotide encoding 5-HT1F) or a testcompound can be immobilized utilizing conjugation of biotin andstreptavidin. Biotinylated 5-HT1F (or a polynucleotide encodingbiotinylated 5-HT1F) or test compounds can be prepared from biotin-NHS(N-hydroxysuccinimide) using techniques well known in the art (e.g.,biotinylation kit, Pierce Chemicals, Rockford, Ill.) and immobilized inthe wells of streptavidin-coated plates (Pierce Chemical).Alternatively, antibodies which specifically bind to 5-HT1F,polynucleotide, or a test compound, but which do not interfere with adesired binding site, such as the active site of 5-HT1F, can bederivatized to the wells of the plate. Unbound target or protein can betrapped in the wells by antibody conjugation.

Methods for detecting such complexes, in addition to those describedabove for the GST-immobilized complexes, include immunodetection ofcomplexes using antibodies which specifically bind to 5-HT1F polypeptideor test compound, enzyme-linked assays which rely on detecting anactivity of 5-HT1F polypeptide, and SDS gel electrophoresis undernon-reducing conditions.

Screening for test compounds which bind to a 5-HT1F polypeptide orpolynucleotide also can be carried out in an intact cell. Any cell whichcomprises a 5-HT1F polypeptide or polynucleotide can be used in acell-based assay system. A 5-HT1F polynucleotide can be naturallyoccurring in the cell or can be introduced using techniques such asthose described above. Binding of the test compound to 5-HT1F or apolynucleotide encoding 5-HT1F is determined as described above.

Functional Assays

Test compounds can be tested for the ability to increase or decrease5-HT1F activity of a 5-HT1F polypeptide. The 5-HT1F activity can bemeasured, for example, using methods described in the specific examples,below. 5-HT1F activity can be measured after contacting either apurified 5-HT1F, a cell membrane preparation, or an intact cell with atest compound. A test compound which decreases 5-HT1F activity by atleast about 10, preferably about 50, more preferably about 75, 90, or100% is identified as a potential agent for decreasing 5-HT1F activity.A test compound which increases 5-HT1F activity by at least about 10,preferably about 50, more preferably about 75, 90, or 100% is identifiedas a potential agent for increasing 5-HT1F activity.

One such screening procedure involves the use of melanophores which aretransfected to express 5-HT1F. Such a screening technique is describedin PCT WO 92/01810 published Feb. 6, 1992. Thus, for example, such anassay may be employed for screening for a compound which inhibitsactivation of the receptor polypeptide of the present invention bycontacting the melanophore cells which encode the receptor with both thereceptor ligand and a compound to be screened. Inhibition of the signalgenerated by the ligand indicates that a compound is a potentialantagonist for the receptor, i.e., inhibits activation of the receptor.The screen may be employed for identifying a compound which activatesthe receptor by contacting such cells with compounds to be screened anddetermining whether each compound generates a signal, i.e., activatesthe receptor.

Other screening techniques include the use of cells which express 5-HT1F(for example, transfected CHO cells) in a system which measuresextracellular pH changes caused by receptor activation [Iwabuchi(1993)]. For example, compounds may be contacted with a cell whichexpresses the receptor polypeptide of the present invention and a secondmessenger response, e.g., signal transduction or pH changes, can bemeasured to determine whether the potential compound activates orinhibits the receptor. Another such screening technique involvesintroducing RNA encoding 5-HT1F into Xenopus oocytes to transientlyexpress the receptor. The receptor oocytes can then be contacted withthe receptor ligand and a compound to be screened, followed by detectionof inhibition or activation of a calcium signal in the case of screeningfor compounds which are thought to inhibit activation of the receptor.

Another screening technique involves expressing 5-HT1F in cells in whichthe receptor is linked to a phospholipase C or D. Such cells includeendothelial cells, smooth muscle cells, embryonic kidney cells, etc. Thescreening may be accomplished as described above by quantifying thedegree of activation of the receptor from changes in the phospholipaseactivity.

Gene Expression

In another embodiment, test compounds which increase or decrease 5-HT1Fgene expression are identified. As used herein, the term “correlateswith expression of a polynucleotide” indicates that the detection of thepresence of nucleic acids, the same or related to a nucleic acidsequence encoding 5-HT1F, by northern analysis or relatime PCR isindicative of the presence of nucleic acids encoding 5-HT1F in a sample,and thereby correlates with expression of the transcript from thepolynucleotide encoding 5-HT1F. The term “microarray”, as used herein,refers to an array of distinct polynucleotides or oligonucleotidesarrayed on a substrate, such as paper, nylon or any other type ofmembrane, filter, chip, glass slide, or any other suitable solidsupport. A 5-HT1F polynucleotide is contacted with a test compound, andthe expression of an RNA or polypeptide product of 5-HT1F polynucleotideis determined. The level of expression of appropriate mRNA orpolypeptide in the presence of the test compound is compared to thelevel of expression of mRNA or polypeptide in the absence of the testcompound. The test compound can then be identified as a regulator ofexpression based on this comparison. For example, when expression ofmRNA or polypeptide is greater in the presence of the test compound thanin its absence, the test compound is identified as a stimulator orenhancer of the mRNA or polypeptide expression. Alternatively, whenexpression of the mRNA or polypeptide is less in the presence of thetest compound than in its absence, the test compound is identified as aninhibitor of the mRNA or polypeptide expression.

The level of 5-HT1F mRNA or polypeptide expression in the cells can bedetermined by methods well known in the art for detecting mRNA orpolypeptide. Either qualitative or quantitative methods can be used. Thepresence of polypeptide products of 5-HT1F polynucleotide can bedetermined, for example, using a variety of techniques known in the art,including immunochemical methods such as radioimmunoassay, Westernblotting, and immunohistochemistry. Alternatively, polypeptide synthesiscan be determined in vivo, in a cell culture, or in an in vitrotranslation system by detecting incorporation of labelled amino acidsinto 5-HT1F.

Such screening can be carried out either in a cell-free assay system orin an intact cell. Any cell which expresses 5-HT1F polynucleotide can beused in a cell-based assay system. The 5-HT1F polynucleotide can benaturally occurring in the cell or can be introduced using techniquessuch as those described above. Either a primary culture or anestablished cell line can be used.

Test Compounds

Suitable test compounds for use in the screening assays of the inventioncan be obtained from any suitable source, e.g., conventional compoundlibraries. The test compounds can also be obtained using any of thenumerous approaches in combinatorial library methods known in the art,including: biological libraries; spatially addressable parallel solidphase or solution phase libraries; synthetic library methods requiringdeconvolution; the “one-bead one-compound” library method; and syntheticlibrary methods using affinity chromatography selection. The biologicallibrary approach is limited to peptide libraries, while the other fourapproaches are applicable to peptide, non-peptide oligomer or smallmolecule libraries of compounds [Lam, (1997)]. Examples of methods forthe synthesis of molecular libraries can be found in the art. Librariesof compounds may be presented in solution or on beads, bacteria, spores,plasmids or phage.

Modeling of Regulators

Computer modeling and searching technologies permit identification ofcompounds, or the improvement of already identified compounds, that canmodulate 5-HT1F expression or activity. Having identified such acompound or composition, the active sites or regions are identified.Such active sites might typically be ligand binding sites, such as theinteraction domain of the ligand with 5-HT1F. The active site can beidentified using methods known in the art including, for example, fromthe amino acid sequences of peptides, from the nucleotide sequences ofnucleic acids, or from study of complexes of the relevant compound orcomposition with its natural ligand. In the latter case, chemical orX-ray crystallographic methods can be used to find the active site byfinding where on the factor the complexed ligand is found.

Next, the three dimensional geometric structure of the active site isdetermined. This can be done by known methods, including X-raycrystallography, which can determine a complete molecular structure. Onthe other hand, solid or liquid phase NMR can be used to determinecertain intramolecular distances. Any other experimental method ofstructure determination can be used to obtain partial or completegeometric structures. The geometric structures may be measured with acomplexed ligand, natural or artificial, which may increase the accuracyof the active site structure determined.

If an incomplete or insufficiently accurate structure is determined, themethods of computer based numerical modeling can be used to complete thestructure or improve its accuracy. Any recognized modeling method may beused, including parameterized models specific to particular biopolymerssuch as proteins or nucleic acids, molecular dynamics models based oncomputing molecular motions, statistical mechanics models based onthermal ensembles, or combined models. For most types of models,standard molecular force fields, representing the forces betweenconstituent atoms and groups, are necessary, and can be selected fromforce fields known in physical chemistry. The incomplete or lessaccurate experimental structures can serve as constraints on thecomplete and more accurate structures computed by these modelingmethods.

Finally, having determined the structure of the active site, eitherexperimentally, by modeling, or by a combination, candidate modulatingcompounds can be identified by searching databases containing compoundsalong with information on their molecular structure. Such a search seekscompounds having structures that match the determined active sitestructure and that interact with the groups defining the active site.Such a search can be manual, but is preferably computer assisted. Thesecompounds found from this search are potential 5-HT1F modulatingcompounds.

Alternatively, these methods can be used to identify improved modulatingcompounds from an already known modulating compound or ligand. Thecomposition of the known compound can be modified and the structuraleffects of modification can be determined using the experimental andcomputer modeling methods described above applied to the newcomposition. The altered structure is then compared to the active sitestructure of the compound to determine if an improved fit or interactionresults. In this manner systematic variations in composition, such as byvarying side groups, can be quickly evaluated to obtain modifiedmodulating compounds or ligands of improved specificity or activity.

Therapeutic Indications and Methods

It was found by the present applicant that 5-HT1F is expressed invarious human tissues.

Neurology

CNS disorders include disorders of the central nervous system as well asdisorders of the peripheral nervous system.

CNS disorders include, but are not limited to brain injuries,cerebrovascular diseases and their consequences, Parkinson's disease,corticobasal degeneration, motor neuron disease, dementia, includingALS, multiple sclerosis, traumatic brain injury, stroke, post-stroke,post-traumatic brain injury, and small-vessel cerebrovascular disease.Dementias, such as Alzheimer's disease, vascular dementia, dementia withLewy bodies, frontotemporal dementia and Parkinsonism linked tochromosome 17, frontotemporal dementias, including Pick's disease,progressive nuclear palsy, corticobasal degeneration, Huntington'sdisease, thalamic degeneration, Creutzfeld-Jakob dementia, HIV dementia,schizophrenia with dementia, and Korsakoff's psychosis, within themeaning of the definition are also considered to be CNS disorders.

Similarly, cognitive-related disorders, such as mild cognitiveimpairment, age-associated memory impairment, age-related cognitivedecline, vascular cognitive impairment, attention deficit disorders,attention deficit hyperactivity disorders, and memory disturbances inchildren with learning disabilities are also considered to be CNSdisorders.

Pain, within the meaning of this definition, is also considered to be aCNS disorder. Pain can be associated with CNS disorders, such asmultiple sclerosis, spinal cord injury, sciatica, failed back surgerysyndrome, traumatic brain injury, epilepsy Parkinson's disease,post-stroke, and vascular lesions in the brain and spinal cord (e.g.,infarct, hemorrhage, vascular malformation). Non-central neuropathicpain includes that associated with post mastectomy pain, phantomfeeling, reflex sympathetic dystrophy (RSD), trigeminalneuralgiaradioculopathy, post-surgical pain, HIV/AIDS related pain,cancer pain, metabolic neuropathies (e.g., diabetic neuropathy,vasculitic neuropathy secondary to connective tissue disease),paraneoplastic polyneuropathy associated, for example, with carcinoma oflung, or leukemia, or lymphoma, or carcinoma of prostate, colon orstomach, trigeminal neuralgia, cranial neuralgias, and post-herpeticneuralgia Pain associated with peripheral nerve damage, central pain(i.e. due to cerebral ischemia) and various chronic pain i.e., lumbago,back pain (low back pain), inflammatory and/or rheumatic pain. Headachepain (for example, migraine with aura, migraine without aura, and othermigraine disorders), episodic and chronic tension-type headache,tension-type like headache, cluster headache, and chronic paroxysmalhemicrania are also CNS disorders.

Visceral pain such as pancreatits, intestinal cystitis, dysmenorrhea,irritable Bowel syndrome, Crohn's disease, biliary colic, ureteralcolic, myocardial infarction and pain syndromes of the pelvic cavity,e.g., vulvodynia, orchialgia, urethral syndrome and protatodynia arealso CNS disorders.

Also considered to be a disorder of the nervous system are acute pain,for example postoperative pain, and pain after trauma.

The human 5-HT1f is highly expressed in the following brain tissues:brain, Alzheimer brain, Alzheimer brain cerebellum, cerebellum (right),cerebellum (left), cerebral cortex, Alzheimer cerebral cortex, frontallobe, Alzheimer brain frontal lobe, occipital lobe, parietal lobe,temporal lobe, substantia nigra, caudatum, corpus callosum, nucleusaccumbens, hippocampus, posteroventral thalamus, dorsalmedial thalamus,hypothalamus, spinal cord (ventral horn), spinal cord (dorsal horn). Theexpression in brain tissues and in particular the differentialexpression between diseased tissue Alzheimer brain and healthy tissuebrain, between diseased tissue Alzheimer brain cerebellum and healthytissue, between diseased tissue Alzheimer cerebral cortex and healthytissue cerebral cortex, between diseased tissue Alzheimer brain frontallobe and healthy tissue frontal lobe demonstrates that the human 5-HT1for mRNA can be utilized to diagnose nervous system diseases.Additionally the activity of the human 5-HT1f can be modulated to treatnervous system diseases.

Cardiovascular Disorders

Heart failure is defined as a pathophysiological state in which anabnormality of cardiac function is responsible for the failure of theheart to pump blood at a rate commensurate with the requirement of themetabolizing tissue. It includes all forms of pumping failures such ashigh-output and low-output, acute and chronic, right-sided orleft-sided, systolic or diastolic, independent of the underlying cause.

Myocardial infarction (MI) is generally caused by an abrupt decrease incoronary blood flow that follows a thrombotic occlusion of a coronaryartery previously narrowed by arteriosclerosis. MI prophylaxis (primaryand secondary prevention) is included as well as the acute treatment ofMI and the prevention of complications.

Ischemic diseases are conditions in which the coronary flow isrestricted resulting in a perfusion which is inadequate to meet themyocardial requirement for oxygen. This group of diseases includesstable angina, unstable angina and asymptomatic ischemia.

Arrhythmias include all forms of atrial and ventriculartachyarrhythmias, atrial tachycardia, atrial flutter, atrialfibrillation, atrio-ventricular reentrant tachycardia, preexitationsyndrome, ventricular tachycardia, ventricular flutter, ventricularfibrillation, as well as bradycardic forms of arrhythmias.

Hypertensive vascular diseases include primary as well as all kinds ofsecondary arterial hypertension, renal, endocrine, neurogenic, others.The genes may be used as drug targets for the treatment of hypertensionas well as for the prevention of all complications arising fromcardiovascular diseases.

Peripheral vascular diseases are defined as vascular diseases in whicharterial and/or venous flow is reduced resulting in an imbalance betweenblood supply and tissue oxygen demand. It includes chronic peripheralarterial occlusive disease (PAOD), acute arterial thrombosis andembolism, inflammatory vascular disorders, Raynaud's phenomenon andvenous disorders.

Atherosclerosis is a cardiovascular disease in which the vessel wall isremodeled, compromising the lumen of the vessel. The atheroscleroticremodeling process involves accumulation of cells, both smooth musclecells and monocyte/macrophage inflammatory cells, in the intima of thevessel wall. These cells take up lipid, likely from the circulation, toform a mature atherosclerotic lesion. Although the formation of theselesions is a chronic process, occurring over decades of an adult humanlife, the majority of the morbidity associated with atherosclerosisoccurs when a lesion ruptures, releasing thrombogenic debris thatrapidly occludes the artery. When such an acute event occurs in thecoronary artery, myocardial infarction can ensue, and in the worst case,can result in death.

The formation of the atherosclerotic lesion can be considered to occurin five overlapping stages such as migration, lipid accumulation,recruitment of inflammatory cells, proliferation of vascular smoothmuscle cells, and extracellular matrix deposition. Each of theseprocesses can be shown to occur in man and in animal models ofatherosclerosis, but the relative contribution of each to the pathologyand clinical significance of the lesion is unclear.

Thus, a need exists for therapeutic methods and agents to treatcardiovascular pathologies, such as atherosclerosis and other conditionsrelated to coronary artery disease.

Cardiovascular diseases include but are not limited to disorders of theheart and the vascular system like congestive heart failure, myocardialinfarction, ischemic diseases of the heart, all kinds of atrial andventricular arrhythmias, hypertensive vascular diseases, peripheralvascular diseases, and atherosclerosis.

Too high or too low levels of fats in the bloodstream, especiallycholesterol; can cause long-term problems. The risk to developatherosclerosis and coronary artery or carotid artery disease (and thusthe risk of having a heart attack or stroke) increases with the totalcholesterol level increasing. Nevertheless, extremely low cholesterollevels may not be healthy. Examples of disorders of lipid metabolism arehyperlipidemia (abnormally high levels of fats (cholesterol,triglycerides, or both) in the blood, may be caused by family history ofhyperlipidemia), obesity, a high-fat diet, lack of exercise, moderate tohigh alcohol consumption, cigarette smoking, poorly controlled diabetes,and an underactive thyroid gland), hereditary hyperlipidemias (type Ihyperlipoproteinemia (familial hyperchylomicronemia), type IIhyperlipoproteinemia (familial hypercholesterolemia), type mhyperlipoproteinemia, type IV hyperlipoproteinemia, or type Vhyperlipoproteinemia), hypolipoproteinemia, lipidoses (caused byabnormalities in the enzymes that metabolize fats), Gaucher's disease,Niemann-Pick disease, Fabry's disease, Wolman's disease,cerebrotendinous xanthomatosis, sitosterolemia, Refsum's disease, orTay-Sachs disease.

Kidney disorders may lead to hypertension or hypotension. Examples forkidney problems possibly leading to hypertension are renal arterystenosis, pyelonephritis, glomerulonephritis, kidney tumors, polycistickidney disease, injury to the kidney, or radiation therapy affecting thekidney. Excessive urination may lead to hypotension.

The human 5-HT1f is highly expressed in the following cardiovascularrelated tissues: heart, pericardium, heart atrium (right), heart atrium(left), heart ventricle (left), heart apex, Purkinje fibers, aortasclerotic, coronary artery sclerotic, pulmonic valve, pulmonary arterysmooth muscle cells, coronary artery endothel cells, iliac arteryendothel cells. Expression in the above mentioned tissues and inparticular the differential expression between diseased tissue aortasclerotic and healthy tissue, between diseased tissue coronary arterysclerotic and healthy tissue coronary artery demonstrates that the human5-HT1f or mRNA can be utilized to diagnose of cardiovascular diseases.Additionally the activity of the human 5-HT1f can be modulated to treatcardiovascular diseases.

Hematological Disorders

Hematological disorders comprise diseases of the blood and all itsconstituents as well as diseases of organs and tissues involved in thegeneration or degradation of all the constituents of the blood. Theyinclude but are not limited to 1) Anemias, 2) MyeloproliferativeDisorders, 3) Hemorrhagic Disorders, 4) Leukopenia, 5) EosinophilicDisorders, 6) Leukemias, 7) Lymphomas, 8) Plasma Cell Dyscrasias, 9).Disorders of the Spleen in the course of hematological disorders.Disorders according to 1) include, but are not limited to anemias due todefective or deficient hem synthesis, deficient erythropoiesis.Disorders according to 2) include, but are not limited to polycythemiavera, tumor-associated erythrocytosis, myelofibrosis, thrombocythenia.Disorders according to 3) include, but are not limited to vasculitis,thrombocytopenia, heparin-induced thrombocytopenia, thromboticthrombocytopenic purpura, hemolytic-uremic syndrome, hereditary andacquired disorders of platelet function, hereditary coagulationdisorders. Disorders according to 4) include, but are not limited toneutropenia, lymphocytopenia. Disorders according to 5) include, but arenot limited to hypereosinophilia, idiopathic hypereosinophilic syndrome.Disorders according to 6) include, but are not limited to acute myeloicleukemia, acute lymphoblastic leukemia, chronic myelocytic leukemia,chronic lymphocytic leukemia, myelodysplastic syndrome. Disordersaccording to 7) include, but are not limited to Hodgkin's disease,non-Hodgkin's lymphoma, Burkitt's lymphoma, mycosis fungoides cutaneousT-cell lymphoma. Disorders according to 8) include, but are not limitedto multiple myeloma, macroglobulinemia, heavy chain diseases. Inextension of the preceding idiopathic thrombocytopenic purpura, irondeficiency anemia, megaloblastic anemia (vitamin B12 deficiency),aplastic anemia, thalassemia, malignant lymphoma bone marrow invasion,malignant lymphoma skin invasion, hemolytic uremic syndrome, giantplatelet disease are considered to be hematological diseases too.

The human 5-HT1f is highly expressed in the following tissues of thehematological system: Jurkat (T-cells), erythrocytes, thymus,thrombocytes, bone marrow CD33+ cells, bone marrow CD34+ cells, bonemarrow CD15+ cells, cord blood CD34+ cells, neutrophils cord blood,neutrophils peripheral blood, spleen. The expression in the abovementioned tissues and in particular the differential expression betweendiseased tissue Jurkat (T-cells) and healthy tissue leukocytes(peripheral blood) demonstrates that the human 5-HT1f or mRNA can beutilized to diagnose of hematological diseases. Additionally theactivity of the human 5-HT1f can be modulated to treat hematologicaldisorders.

Gastrointestinal and Liver Diseases

Gastrointestinal diseases comprise primary or secondary, acute orchronic diseases of the organs of the gastrointestinal tract which maybe acquired or inherited, benign or malignant or metaplastic, and whichmay affect the organs of the gastrointestinal tract or the body as awhole. They comprise but are not limited to 1) disorders of theesophagus like achalasia, vigoruos achalasia, dysphagia, cricopharyngealincoordination, pre-esophageal dysphagia, diffuse esophageal spasm,globus sensation, Barrett's metaplasia, gastroesophageal reflux, 2)disorders of the stomach and duodenum like functional dyspepsia,inflammation of the gastric mucosa, gastritis, stress gastritis, chronicerosive gastritis, atrophy of gastric glands, metaplasia of gastrictissues, gastric ulcers, duodenal ulcers, neoplasms of the stomach, 3)disorders of the pancreas like acute or chronic pancreatitis,insufficiency of the exocrinic or endocrinic tissues of the pancreaslike steatorrhea, diabetes, neoplasms of the exocrine or endocrinepancreas like 3.1) multiple endocrine neoplasia syndrome, ductaladenocarcinoma, cystadenocarcinoma, islet cell tumors, insulnoma,gastrinoma, carcinoid tumors, glucagonoma, Zollinger-Ellison syndrome,Vipoma syndrome, malabsorption syndrome, 4) disorders of the bowel likechronic inflammatory diseases of the bowel, Crohn's disease, ileus,diarrhea and constipation, colonic inertia, megacolon, malabsorptionsyndrome, ulcerative colitis, 4.1) functional bowel disorders likeirritable bowel syndrome, 4.2) neoplasms of the bowel like familialpolyposis, adenocarcinoma, primary malignant lymphoma, carcinoid tumors,Kaposi's sarcoma, polyps, cancer of the colon and rectum.

Liver diseases comprise primary or secondary, acute or chronic diseasesor injury of the liver which may be acquired or inherited, benign ormalignant, and which may affect the liver or the body as a whole. Theycomprise but are not limited to disorders of the bilirubin metabolism,jaundice, syndroms of Gilbert's, Crigler-Najjar, DubinJohnson and Rotor,intrahepatic cholestasis, hepatomegaly, portal hypertension, ascites,Budd-Chiari syndrome, portal-systemic encephalopathy, fatty liver,steatosis, Reye's syndrome, liver diseases due to alcohol, alcoholichepatitis or cirrhosis, fibrosis and cirrhosis, fibrosis and cirrhosisof the liver due to inborn errors of metabolism or exogenous substances,storage diseases, syndromes of Gaucher's, Zellweger's, Wilson's-disease,acute or chronic hepatitis, viral hepatitis and its variants,inflammatory conditions of the liver due to viruses, bacteria, fungi,protozoa, helminths; drug induced disorders of the liver, chronic liverdiseases like primary sclerosing cholangitis,alpha₁-antitrypsin-deficiency, primary biliary cirrhosis, postoperativeliver disorders like postoperative intrahepatic cholestasis, hepaticgranulomas, vascular liver disorders associated with systemic disease,benign or malignant neoplasms of the liver, disturbance of livermetabolism in the new-born or prematurely born.

The human 5-HT1f is highly expressed in the following tissues of thegastroenterological system: rectum, liver liver cirrhosis. Theexpression in the above mentioned tissues and in particular thedifferential expression between diseased tissue liver liver cirrhosisand healthy tissue liver demonstrates that the human 5-HT1f or mRNA canbe utilized to diagnose of gastroenterological disorders. Additionallythe activity of the human 5-HT1f can be modulated to treatgastroenterological disorders.

Musculoskeletal Diseases

Components of the musculoskeletal system are skeleton, muscles, tendons,ligaments, and other components of joints. Disorders of themusculoskeletal system often cause chronic pain and physical disability.They range from injures, infsctions, inflammation or other types ofdisorders. Examples of musculoskeletal disorders are presented in thefollowing.

Examples are osteoporosis, postnenopausal osteoporosis, senileosteoporosis, secondary osteoporosis, idiopathic juvenile osteoporosis,Paget's disease of the bone, osteochondromas (osteocartilaginousexostoses), tumors of the bone (benign chondromas, chondroblastomas,chondromyxoid fibromas, osteoid osteomas, giant cell tumors of the bone,multiple myeloma, osteosarcoma (osteogenic sarcoma), fibrosarcomas andmalignant fibrous histiocytomas, chondrosarcomas, Ewing's tumor (Ewing'ssarcoma), malignant lymphoma of bone (reticulum cell sarcoma, metastatictumors of the bone), osteoarthritis, and gout and Pseudogout.

Examples of disorders of joints and connective tissue are rheumatoidarthritis, psoriatic arthritis, discoid lupus erythematosus, systemiclupus erythematosus, scleroderma (systemic sclerosis), Sjrögren'ssyndrome, connective tissue disease, polymyositis and dermatomyositis,relapsing polychondritis, vasculitis, polyarteritis nodosa, polymyalgiarheumatica, temporal arteritis, Wegener's granulomatosis, Reiter'ssyndrome, Behçet's syndrome, ankylosing spondylitis, or Charcot's joints(neuropathic joint disease).

Eamples for bone and joint infections are osteomyelitis, and infectiousarthritis.

Examples of disorders of muscles, bursas, and tendons are spasmodictorticollis, fibromyalgia syndromes (myofascial pain syndromes,fibromyositis), bursitis, tendinitis and tenosynovitis.

Foot problems are, for example ankle sprain, foot fractures, heel spurs,Sever's disease, posterior achilles tendon bursitis, anterior achillestendon bursitis, posterior tibial neuralgia, pain in the ball of thefoot (caused by damage to the nerves between the toes or to the jointsbetween the toes and foot), onychomycosis, or nail discoloration.

The human 5-HT1f is highly expressed in the following muscle/skeletontissues: cartilage, bone connective tissue, adipose. The expression inmuscle/skleleton tissues demonstrates that the human 5-HT1f or mRNA canbe utilized to diagnose of diseases of the muscle/skeleton system.Additionally the activity of the human 5-HT1f can be modulated to treatthose diseases.

Cancer Disorders.

Cancer disorders within the scope of this definition comprise anydisease of an organ or tissue in mammals characterized by poorlycontrolled or uncontrolled multiplication of normal or abnormal cells inthat tissue and its effect on the body as a whole. Cancer diseaseswithin the scope of the definition comprise benign neoplasms,dysplasias, hyperplasias as well as neoplasms showing metastatic growthor any other transformations like e.g. leukoplakias which often precedea breakout of cancer. Cells and tissues are cancerous when they growmore rapidly than normal cells, displacing or spreading into thesurrounding healthy tissue or any other tissues of the body described asmetastatic growth, assume abnormal shapes and sizes, show changes intheir nucleocytoplasmatic ratio, nuclear polychromasia, and finally maycease. Cancerous cells and tissues may affect the body as a whole whencausing paraneoplastic syndromes or if cancer occurs within a vitalorgan or tissue, normal function will be impaired or halted, withpossible fatal results. The ultimate involvement of a vital organ bycancer, either primary or metastatic, may lead to the death of themammal affected. Cancer tends to spread, and the extent of its spread isusually related to an individual's chances of surviving the disease.Cancers are generally said to be in one of three stages of growth:early, or localized, when a tumor is still confined to the tissue oforigin, or primary site; direct extension, where cancer cells from thetumour have invaded adjacent tissue or have spread only to regionallymph nodes; or metastasis, in which cancer cells have migrated todistant parts of the body from the primary site, via the blood or lymphsystems, and have established secondary sites of infection. Cancer issaid to be malignant because of its tendency to cause death if nottreated. Benign tumors usually do not cause death, although they may ifthey interfere with a normal body function by virtue of their location,size, or paraneoplastic side effects. Hence benign tumors fall under thedefinition of cancer within the scope of this definition as well. Ingeneral, cancer cells divide at a higher rate than do normal cells, butthe distinction between the growth of cancerous and normal tissues isnot so much the rapidity of cell division in the former as it is thepartial or complete loss of growth restraint in cancer cells and theirfailure to differentiate into a useful, limited tissue of the type thatcharacterizes the functional equilibrium of growth of normal tissue.Cancer tissues may express certain molecular receptors and probably areinfluenced by the host's susceptibility and immunity and it is knownthat certain cancers of the breast and prostate, for example, areconsidered dependent on specific hormones for their existence. The term“cancer” under the scope of the definition is not limited to simplebenign neoplasia but comprises any other benign and malign neoplasialike 1) Carcinoma, 2) Sarcoma, 3) Carcinosarcoma, 4) Cancers of theblood-forming tissues, 5) tumors of nerve tissues including the brain,6) cancer of skin cells. Cancer according to 1) occurs in epithelialtissues, which cover the outer body (the skin) and line mucous membranesand the inner cavitary structures of organs e.g. such as the breast,lung, the respiratory and gastrointestinal tracts, the endocrine glands,and the genitourinary system. Ductal or glandular elements may persistin epithelial tumors, as in adenocarcinomas like e.g. thyroidadenocarcinoma, gastric adenocarcinoma, uterine adenocarcinoma. Cancersof the pavement-cell epithelium of the skin and of certain mucousmembranes, such as e.g. cancers of the tongue, lip, larynx, urinarybladder, uterine cervix, or penis, may be termed epidermoid orsquamous-cell carcinomas of the respective tissues and are in the scopeof the definition of cancer as well. Cancer according to 2) develops inconnective tissues, including fibrous tissues, adipose (fat) tissues,muscle, blood vessels, bone, and cartilage like e.g. osteogenic sarcoma;liposarcoma, fibrosarcoma, synovial sarcoma. Cancer according to 3) iscancer that develops in both epithelial and connective tissue. Cancerdisease within the scope of this definition may be primary or secondary,whereby primary indicates that the cancer originated in the tissue whereit is found rather than was established as a secondary site throughmetastasis from another lesion. Cancers and tumor diseases within thescope of this definition may be benign or malign and may affect allanatomical structures of the body of a mammal. By example but notlimited to they comprise cancers and tumor diseases of I) the bonemarrow and bone marrow derived cells (leukemias), II) the endocrine andexocrine glands like e.g. thyroid, parathyroid, pituitary, adrenalglands, salivary glands, pancreas III) the breast, like e.g. benign ormalignant tumors in the mammary glands of either a male or a female, themammary ducts, adenocarcinoma, medullary carcinoma, comedo carcinoma,Paget's disease of the nipple, inflammatory carcinoma of the youngwoman, IV) the lung, V) the stomach, VI) the liver and spleen, VI) thesmall intestine, VI) the colon, IX) the bone and its supportive andconnective tissues like malignant or benign bone tumour, e.g. malignantosteogenic sarcoma, benign osteoma, cartilage tumors; like malignantchondrosarcoma or benign chondroma; bone marrow tumors like malignantmyeloma or benign eosinophilic granuloma, as well as metastatic tumorsfrom bone tissues at other locations of the body; X) the mouth, throat,larynx, and the esophagus, XI) the urinary bladder and the internal andexternal organs and structures of the urogenital system of male andfemale like ovaries, uterus, cervix of the uterus, testes, and prostategland, XI) the prostate, X) the pancreas, like ductal carcinoma of thepancreas; XIV) the lymphatic tissue like lymphomas and other tumors oflymphoid origin, XV) the skin, XVI) cancers and tumor diseases of allanatomical structures belonging to the respiration and respiratorysystems including thoracal muscles and linings, XVII) primary orsecondary cancer of the lymph nodes XVII) the tongue and of the bonystructures of the hard palate or sinuses, XVIV) the mouth, cheeks, neckand salivary glands, XX) the blood vessels including the heart and theirlinings, XXI) the smooth or skeletal muscles and their ligaments andlinings, XXII) the peripheral, the autonomous, the central nervoussystem including the cerebellum, XXIII) the adipose tissue.

The human 5-HT1f is highly expressed in the following cancer tissues:Jurkat (T-cells), lung tumor, ovary tumor, prostate. The expression inthe above mentioned tissues and in particular the differentialexpression between diseased tissue Jurkat (T-cells) and healthy tissueleukocytes (peripheral blood), between diseased tissue lung tumor andhealthy tissue lung, between diseased tissue ovary tumor and healthytissue ovary demonstrates that the human 5-HT1f or mRNA can be utilizedto diagnose of cancer. Additionally the activity of the human 5-HT1f canbe modulated to treat cancer.

Disorders Related to Pulmology

Asthma is thought to arise as a result of interactions between multiplegenetic and environmental factors and is characterized by three majorfeatures: 1) intermittent and reversible airway obstruction caused bybronchoconstriction, increased mucus production, and thickening of thewalls of the airways that leads to a narrowing of the airways, 2) airwayhyperresponsiveness, and 3) airway inflammation. Certain cells arecritical to the inflammatory reaction of asthma and they include T cellsand antigen presenting cells, B cells that produce IgE, and mast cells,basophils, eosinophils, and other cells that bind IgE. These effectorcells accumulate at the site of allergic reaction in the airways andrelease toxic products that contribute to the acute pathology andeventually to tissue destruction related to the disorder. Other residentcells, such as smooth muscle cells, lung epithelial cells,mucus-producing cells, and nerve cells may also be abnormal inindividuals with asthma and may contribute to its pathology. While theairway obstruction of asthma, presenting clinically as an intermittentwheeze and shortness of breath, is generally the most pressing symptomof the disease requiring immediate treatment, the inflammation andtissue destruction associated with the disease can lead to irreversiblechanges that eventually make asthma a chronic and disabling disorderrequiring long-term management.

Chronic obstructive pulmonary (or airways) disease (COPD) is a conditiondefined physiologically as airflow obstruction that generally resultsfrom a mixture of emphysema and peripheral airway obstruction due tochronic bronchitis [Botstein, 1980]. Emphysema is characterised bydestruction of alveolar walls leading to abnormal enlargement of the airspaces of the lung. Chronic bronchitis is defined clinically as thepresence of chronic productive cough for three months in each of twosuccessive years. In COPD, airflow obstruction is usually progressiveand is only partially reversible. By far the most important risk factorfor development of COPD is cigarette smoking, although the disease doesalso occur in non-smokers.

The human 5-HT1f is highly expressed in the following tissues of therespiratory system: pulmonary artery smooth muscle cells, bone marrowCD15+ cells, neutrophils cord blood, neutrophils peripheral blood, lungright mid lobe, lung right lower lobe, lung tumor, primary bronchia,secondary bronchia, bronchial epithelial cells, bronchial smooth musclecells. The expression in the above mentioned tissues and in particularthe differential expression between diseased tissue lung tumor andhealthy tissue lung demonstrates that the human 5-HT1f or mRNA can beutilized to diagnose of respiratory diseases. Additionally the activityof the human 5-HT1f can be modulated to treat those diseases.

Disorders Related to Urology

Genitourinary disorders comprise benign and malign disorders of theorgans constituting the genitourinary system of female and male, renaldiseases like acute or chronic renal failure, immunologically mediatedrenal diseases like renal transplant rejection, lupus nephritis, immunecomplex renal diseases, glomerulopathies, nephritis, toxic nephropathy,obstructive uropathies like benign prostatic hyperplasia (BPH),neurogenic bladder syndrome, urinary incontinence like urge-, stress-,or overflow incontinence, pelvic pain, and erectile dysfunction.

The human 5-HT1f is highly expressed in the following urologicaltissues: prostate, prostate BPH, prostate tumor, penis, fetal kidney,renal epithelial cells. The expression in the above mentioned tissuesand in particular the differential expression between diseased tissueprostate BPH and healthy tissue prostate, between diseased tissueprostate tumor and healthy tissue prostate demonstrates that the human5-HT1f or mRNA can be utilized to diagnose of urological disorders.Additionally the activity of the human 5-HT1f can be modulated to treaturological disorders.

Applications

The present invention provides for both prophylactic and therapeuticmethods for hematological diseases, disorders of the peripheral andcentral nervous system, gastrointestinal diseases, cardiovasculardiseases, cancer, muscle/skeleton disorders, respiratory diseases andurological diseases.

The regulatory method of the invention involves contacting a cell withan agent that modulates one or more of the activities of 5-HT1F. Anagent that modulates activity can be an agent as described herein, suchas a nucleic acid or a protein, a naturally-occurring cognate ligand ofthe polypeptide, a peptide, a peptidomimetic, or any small molecule. Inone embodiment, the agent stimulates one or more of the biologicalactivities of 5-HT1F. Examples of such stimulatory agents include theactive 5-HT1F and nucleic acid molecules encoding a portion of 5-HT1F.In another embodiment, the agent inhibits one or more of the biologicalactivities of 5-HT1F. Examples of such inhibitory agents includeantisense nucleic acid molecules and antibodies. These regulatorymethods can be performed in vitro (e.g., by culturing the cell with theagent) or, alternatively, in vivo (e.g, by administering the agent to asubject). As such, the present invention provides methods of treating anindividual afflicted with a disease or disorder characterized byunwanted expression or activity of 5-HT1F or a protein in the 5-HT1Fsignaling pathway. In one embodiment, the method involves administeringan agent like any agent identified or being identifiable by a screeningassay as described herein, or combination of such agents that modulatesay upregulate or downregulate the expression or activity of 5-HT1F orof any protein in the 5-HT1F signaling pathway. In another embodiment,the method involves administering a regulator of 5-HT1F as therapy tocompensate for reduced or undesirably low expression or activity ofS-HT1F or a protein in the 5-HT1F signaling pathway.

Stimulation of activity or expression of 5-HT1F is desirable insituations in which activity or expression is abnormally low and inwhich increased activity is likely to have a beneficial effect.Conversely, inhibition of activity or expression of 5-HT1F is desirablein situations in which activity or expression of 5-HT1F is abnormallyhigh and in which decreasing its activity is likely to have a beneficialeffect.

This invention is further illustrated by the following examples whichshould not be construed as limiting. The contents of all references,patents and published patent applications cited throughout thisapplication are hereby incorporated by reference.

Pharmaceutical Compositions

This invention further pertains to novel agents identified by theabove-described screening assays and uses thereof for treatments asdescribed herein.

The nucleic acid molecules, polypeptides, and antibodies (also referredto herein as “active compounds”) of the invention can be incorporatedinto pharmaceutical compositions suitable for administration. Suchcompositions typically comprise the nucleic acid molecule, protein, orantibody and a pharmaceutically acceptable carrier. As used herein thelanguage “pharmaceutically acceptable carrier” is intended to includeany and all solvents, dispersion media, coatings, antibacterial andantifungal agents, isotonic and absorption delaying agents, and thelike, compatible with pharmaceutical administration. The use of suchmedia and agents for pharmaceutically active substances is well known inthe art. Except insofar as any conventional media or agent isincompatible with the active compound, use thereof in the compositionsis contemplated. Supplementary active compounds can also be incorporatedinto the compositions.

The invention includes pharmaceutical compositions comprising aregulator of 5-HT1F expression or activity (and/or a regulator of theactivity or expression of a protein in the 5-HT1F signaling pathway) aswell as methods for preparing such compositions by combining one or moresuch regulators and a pharmaceutically acceptable carrier. Also withinthe invention are pharmaceutical compositions comprising a regulatoridentified using the screening assays of the invention packaged withinstructions for use. For regulators that are antagonists of 5-HT1Factivity or which reduce 5-HT1F expression, the instructions wouldspecify use of the pharmaceutical composition for treatment ofhematological and cardiovascular diseases, disorders of the peripheraland central nervous system, COPD, asthma, genito-urological disordersand inflammation diseases. For regulators that are agonists of 5-HT1Factivity or increase 5-HT1F expression, the instructions would specifyuse of the pharmaceutical composition for treatment of hematological andcardiovascular diseases, disorders of the peripheral and central nervoussystem, COPD, asthma, genito-urological disorders and inflammationdiseases.

An antagonist of 5-HT1F may be produced using methods which aregenerally known in the art. In particular, purified 5-HT1F may be usedto produce antibodies or to screen libraries of pharmaceutical agents toidentify those which specifically bind 5-HT1F. Antibodies to 5-HT1F mayalso be generated using methods that are well known in the art. Suchantibodies may include, but are not limited to, polyclonal, monoclonal,chimeric, single chain antibodies, Fab fragments, and fragments producedby a Fab expression library. Neutralizing antibodies like those whichinhibit dimer formation are especially preferred for therapeutic use.

In another embodiment of the invention, the polynucleotides encoding5-HT1F, or any fragment or complement thereof, may be used fortherapeutic purposes. In one aspect, the complement of thepolynucleotide encoding 5-HT1F may be used in situations in which itwould be desirable to block the transcription of the mRNA. Inparticular, cells may be transformed with sequences complementary topolynucleotides encoding 5-HT1F. Thus, complementary molecules orfragments may be used to modulate 5-HT1F activity, or to achieveregulation of gene function. Such technology is now well known in theart, and sense or antisense oligonucleotides or larger fragments can bedesigned from various locations along the coding or control regions ofsequences encoding 5-HT1F.

Expression vectors derived from retroviruses, adenoviruses, or herpes orvaccinia viruses, or from various bacterial plasmids, may be used fordelivery of nucleotide sequences to the targeted organ, tissue, or cellpopulation. Methods which are well known to those skilled in the art canbe used to construct vectors which will express nucleic acid sequencecomplementary to the polynucleotides of the gene encoding 5-HT1F. Thesetechniques are described, for example, in [Scott and Smith (1990)Science 249:386-390].

Any of the therapeutic methods described above may be applied to anysubject in need of such therapy, including, for example, mammals such asdogs, cats, cows, horses, rabbits, monkeys, and most preferably, humans.

An additional embodiment of the invention relates to the administrationof a pharmaceutical composition containing 5-HT1F in conjunction with apharmaceutically acceptable carrier, for any of the therapeutic effectsdiscussed above. Such pharmaceutical compositions may consist of 5-HT1F,antibodies to 5-HT1F, and mimetics, agonists, antagonists, or inhibitorsof 5-HT1F. The compositions may be administered alone or in combinationwith at least one other agent, such as a stabilizing compound, which maybe administered in any sterile, biocompatible pharmaceutical carrierincluding, but not limited to, saline, buffered saline, dextrose, andwater. The compositions may be administered to a patient alone, or incombination with other agents, drugs or hormones.

A pharmaceutical composition of the invention is formulated to becompatible with its intended route of administration. Examples of routesof administration include parenteral, e.g., intravenous, intradermal,subcutaneous, oral (e.g., inhalation), transdermal (topical),transmucosal, and rectal administration. Solutions or suspensions usedfor parenteral, intradermal, or subcutaneous application can include thefollowing components: a sterile diluent such as water for injection,saline solution, fixed oils, polyethylene glycols, glycerine, propyleneglycol or other synthetic solvents; antibacterial agents such as benzylalcohol or methyl parabens; antioxidants such as ascorbic acid or sodiumbisulfite; chelating agents such as ethylenediaminetetraacetic acid;buffers such as acetates, citrates or phosphates and agents for theadjustment of tonicity such as sodium chloride or dextrose. pH can beadjusted with acids or bases, such as hydrochloric acid or sodiumhydroxide. The parenteral preparation can be enclosed in ampoules,disposable syringes or multiple dose vials made of glass or plastic.

Pharmaceutical compositions suitable for injectable use include sterileaqueous solutions (where water soluble) or dispersions and sterilepowders for the extemporaneous preparation of sterile injectablesolutions or dispersions. For intravenous administration, suitablecarriers include physiological saline, bacteriostatic water, CremophorEM™ (BASF, Parsippany, N.J.) or phosphate buffered saline (PBS). In allcases, the composition must be sterile and should be fluid to the extentthat easy syringability exists. It must be stable under the conditionsof manufacture and storage and must be preserved against thecontaminating action of microorganisms such as bacteria and fungi. Thecarrier can be a solvent or dispersion medium containing, for example,water, ethanol, a pharmaceutically acceptable polyol like glycerol,propylene glycol, liquid polyetheylene glycol, and suitable mixturesthereof. The proper fluidity can be maintained, for example, by the useof a coating such as lecithin, by the maintenance of the requiredparticle size in the case of dispersion and by the use of surfactants.Prevention of the action of microorganisms can be achieved by variousantibacterial and antifungal agents, for example, parabens,chlorobutanol, phenol, ascorbic acid, thimerosal, and the like. In manycases, it will be preferable to include isotonic agents, for example,sugars, polyalcohols such as mannitol, sorbitol, sodium chloride in thecomposition. Prolonged absorption of the injectable compositions can bebrought about by including in the composition an agent which delaysabsorption, for example, aluminum monostearate and gelatin. Sterileinjectable solutions can be prepared by incorporating the activecompound (e.g., a polypeptide or antibody) in the required amount in anappropriate solvent with one or a combination of ingredients enumeratedabove, as required, followed by filtered sterilization. Generally,dispersions are prepared by incorporating the active compound into asterile vehicle which contains a basic dispersion medium and therequired other ingredients from those enumerated above. In the case ofsterile powders for the preparation of sterile injectable solutions, thepreferred methods of preparation are vacuum drying and freeze-dryingwhich yields a powder of the active ingredient plus any additionaldesired ingredient from a previously sterile-filtered solution thereof.

Oral compositions generally include an inert diluent or an ediblecarrier. They can be enclosed in gelatin capsules or compressed intotablets. For the purpose of oral therapeutic administration, the activecompound can be incorporated with excipients and used in the form oftablets, troches, or capsules. Oral compositions can also be preparedusing a fluid carrier for use as a mouthwash, wherein the compound inthe fluid carrier is applied orally and swished and expectorated orswallowed.

Pharmaceutically compatible binding agents, and/or adjuvant materialscan be included as part of the composition. The tablets, pills,capsules, troches and the like can contain any of the followingingredients, or compounds of a similar nature: a binder such asmicrocrystalline cellulose, gum tragacanth or gelatin; an excipient suchas starch or lactose, a disintegrating agent such as alginic acid,Primogel, or corn starch; a lubricant such as magnesium stearate orsterotes; a glidant such as colloidal silicon dioxide; a sweeteningagent such as sucrose or saccharin; or a flavoring agent such aspeppermint, methyl salicylate, or orange flavoring.

For administration by inhalation, the compounds are delivered in theform of an aerosol spray from a pressurized container or dispenser whichcontains a suitable propellant, e.g., a gas such as carbon dioxide, or anebulizer.

Systemic administration can also be by transmucosal or transdermalmeans. For transmucosal or transdermal administration, penetrantsappropriate to the barrier to be permeated are used in the formulation.Such penetrants are generally known in the art, and include, forexample, for transmucosal administration, detergents, bile salts, andfusidic acid derivatives. Transmucosal administration can beaccomplished through the use of nasal sprays or suppositories. Fortransdermal administration, the active compounds are formulated intoointments, salves, gels, or creams as generally known in the art.

The compounds can also be prepared in the form of suppositories (e.g.,with conventional suppository bases such as cocoa butter and otherglycerides) or retention enemas for rectal delivery.

In one embodiment, the active compounds are prepared with carriers thatwill protect the compound against rapid elimination from the body, suchas a controlled release formulation, including implants andmicroencapsulated delivery systems. Biodegradable, biocompatiblepolymers can be used, such as ethylene vinyl acetate, polyanhydrides,polyglycolic acid, collagen, polyorthoesters, and polylactic acid.Methods for preparation of such formulations will be apparent to thoseskilled in the art. The materials can also be obtained commercially fromAlza Corporation and Nova Pharmaceuticals, Inc. Liposomal suspensions(including liposomes targeted to infected cells with monoclonalantibodies to viral antigens) can also be used as pharmaceuticallyacceptable carriers. These can be prepared according to methods known tothose skilled in the art, for example, as described in U.S. Pat. No.4,522,811.

It is especially advantageous to formulate oral or parenteralcompositions in dosage unit form for ease of administration anduniformity of dosage. Dosage unit form as used herein refers tophysically discrete units suited as unitary dosages for the subject tobe treated; each unit containing a predetermined quantity of activecompound calculated to produce the desired therapeutic effect inassociation with the required pharmaceutical carrier. The specificationfor the dosage unit forms of the invention are dictated by and directlydependent on the unique characteristics of the active compound and theparticular therapeutic effect to be achieved, and the limitationsinherent in the art of compounding such an active compound for thetreatment of individuals.

The pharmaceutical compositions can be included in a container, pack, ordispenser together with instructions for administration. Forpharmaceutical compositions which include an antagonist of 5-HT1Factivity, a compound which reduces expression of 5-HT1F, or a compoundwhich reduces expression or activity of a protein in the 5-HT1Fsignaling pathway or any combination thereof, the instructions foradministration will specify use of the composition for hematological andcardiovascular diseases, disorders of the peripheral and central nervoussystem, COPD, asthma, genito-urological disorders and inflammationdiseases. For pharmaceutical compositions which include an agonist of5-HT1F activity, a compound which increases expression of 5-HT1F, or acompound which increases expression or activity of a protein in the5-HT1F signaling pathway or any combination thereof, the instructionsfor administration will specify use of the composition for hematologicaland cardiovascular diseases, disorders of the peripheral and centralnervous system, COPD, asthma, genito-urological disorders andinflammation diseases.

Diagnostics

In another embodiment, antibodies which specifically bind 5-HT1F may beused for the diagnosis of disorders characterized by the expression of5-HT1F, or in assays to monitor patients being treated with 5-HT1F oragonists, antagonists, and inhibitors of 5-HT1F. Antibodies useful fordiagnostic purposes may be prepared in the same manner as thosedescribed above for therapeutics. Diagnostic assays for 5-HT1F includemethods which utilize the antibody and a label to detect 5-HT1F in humanbody fluids or in extracts of cells or tissues. The antibodies may beused with or without modification, and may be labeled by covalent ornon-covalent joining with a reporter molecule. A wide variety ofreporter molecules, several of which are described above, are known inthe art and may be used.

A variety of protocols for measuring 5-HT1F, including ELISAs, RLAs, andFACS, are known in the art and provide a basis for diagnosing altered orabnormal levels of 5-HT1F expression. Normal or standard values for5-HT1F expression are established by combining body fluids or cellextracts taken from normal mammalian subjects, preferably human, withantibody to 5-HT1F under conditions suitable for complex formation Theamount of standard complex formation may be quantified by variousmethods, preferably by photometric means. Quantities of 5-HT1F expressedin subject samples from biopsied tissues are compared with the standardvalues. Deviation between standard and subject values establishes theparameters for diagnosing disease.

In another embodiment of the invention, the polynucleotides encoding5-HT1F may be used for diagnostic purposes. The polynucleotides whichmay be used include oligonucleotide sequences, complementary RNA and DNAmolecules, and PNAs. The polynucleotides may be used to detect andquantitate gene expression in biopsied tissues in which expression of5-HT1F may be correlated with disease. The diagnostic assay may be usedto distinguish between absence, presence, and excess expression of5-HT1F, and to monitor regulation of 5-HT1F levels during therapeuticintervention.

Polynucleotide sequences encoding 5-HT1F may be used for the diagnosisof hematological diseases, disorders of the peripheral and centralnervous system, gastrointestinal diseases, cardiovascular diseases,cancer, muscle/skeleton disorders, respiratory diseases and urologicaldiseases associated with expression of 5-HT1F. The polynucleotidesequences encoding 5-HT1F may be used in Southern, Northern, or dot-blotanalysis, or other membrane-based technologies; in PCR technologies; indipstick, pin, and ELISA assays; and in microarrays utilizing fluids ortissues from patient biopsies to detect altered 5-HT1F expression. Suchqualitative or quantitative methods are well known in the art.

In a particular aspect, the nucleotide sequences encoding 5-HT1F may beuseful in assays that detect the presence of associated disorders,particularly those mentioned above. The nucleotide sequences encoding5-HT1F may be labelled by standard methods and added to a fluid ortissue sample from a patient under conditions suitable for the formationof hybridization complexes. After a suitable incubation period, thesample is washed and the signal is quantitated and compared with astandard value. If the amount of signal in the patient sample issignificantly altered from that of a comparable control sample, thenucleotide sequences have hybridized with nucleotide sequences in thesample, and the presence of altered levels of nucleotide sequencesencoding 5-HT1F in the sample indicates the presence of the associateddisorder. Such assays may also be used to evaluate the efficacy of aparticular therapeutic treatment regimen in animal studies, in clinicaltrials, or in monitoring the treatment of an individual patient.

In order to provide a basis for the diagnosis of hematological diseases,disorders of the peripheral and central nervous system, gastrointestinaldiseases, cardiovascular diseases, cancer, muscle/skeleton disorders,respiratory diseases and urological diseases associated with expressionof 5-HT1F, a normal or standard profile for expression is established.This may be accomplished by combining body fluids or cell extracts takenfrom normal subjects, either animal or human, with a sequence, or afragment thereof, encoding 5-HT1F, under conditions suitable forhybridization or amplification. Standard hybridization may be quantifiedby comparing the values obtained from normal subjects with values froman experiment in which a known amount of a substantially purifiedpolynucleotide is used. Standard values obtained from normal samples maybe compared with values obtained from samples from patients who aresymptomatic for a disorder. Deviation from standard values is used toestablish the presence of a disorder.

Another technique for drug screening which may be used provides for highthroughput screening of compounds having suitable binding affinity tothe protein of interest as described in published PCT applicationWO84/03564. In this method, large numbers of different small testcompounds are synthesized on a solid substrate, such as plastic pins orsome other surface. The test compounds are reacted with 5-HT1F, orfragments thereof, and washed. Bound 5-HT1F is then detected by methodswell known in the art. Purified 5-HT1F can also be coated directly ontoplates for use in the aforementioned drug screening techniques.Alternatively, non-neutralizing antibodies can be used to capture thepeptide and immobilize it on a solid support.

In another embodiment, one may use competitive drug screening assays inwhich neutralizing antibodies capable of binding 5-HT1F specificallycompete with a test-compound for binding 5-HT1F. In this manner,antibodies can be used to detect the presence of any peptide whichshares one or more antigenic determinants with 5-HT1F.

G-protein coupled receptors are ubiquitous in the mammalian host and areresponsible for many biological functions, including many pathologies.Accordingly, it is desirable to find compounds and drugs which stimulatea G-protein coupled receptor on the one hand and which can inhibit thefunction of a G-protein coupled receptor on the other hand. For example,compounds which activate the G-protein coupled receptor may be employedfor therapeutic purposes, such as the treatment of asthma, Parkinson'sdisease, acute heart failure, urinary retention, and osteoporosis. Inparticular, compounds which activate the receptors of the presentinvention are useful in treating various cardiovascular ailments such ascaused by the lack of pulmonary blood flow or hypertension. In additionthese compounds may also be used in treating various physiologicaldisorders relating to abnormal control of fluid and electrolytehomeostasis and in diseases associated with abnormal angiotensin-inducedaldosterone secretion.

In general, compounds which inhibit activation of the G-protein coupledreceptor may be employed for a variety of therapeutic purposes, forexample, for the treatment of hypotension and/or hypertension, anginapectoris, myocardial infarction, ulcers, asthma, allergies, benignprostatic hypertrophy, and psychotic and neurological disordersincluding schizophrenia, manic excitement, depression, delirium,dementia or severe mental retardation, dyskinesias, such as Huntington'sdisease or Tourett's syndrome, among others. Compounds which inhibitG-protein coupled receptors have also been useful in reversingendogenous anorexia and in the control of bulimia.

Determination of a Therapeutically Effective Dose

The determination of a therapeutically effective dose is well within thecapability of those skilled in the art. A therapeutically effective doserefers to that amount of active ingredient which increases or decreases5-HT1F activity relative to 5-HT1F activity which occurs in the absenceof the therapeutically effective dose. For any compound, thetherapeutically effective dose can be estimated initially either in cellculture assays or in animal models, usually mice, rabbits, dogs, orpigs. The animal model also can be used to determine the appropriateconcentration range and route of administration. Such information canthen be used to determine useful doses and routes for administration inhumans.

Therapeutic efficacy and toxicity, e.g., ED₅₀ (the dose therapeuticallyeffective in 50% of the population) and LD₅₀ (the dose lethal to 50% ofthe population), can be determined by standard pharmaceutical proceduresin cell cultures or experimental animals. The dose ratio of toxic totherapeutic effects is the therapeutic index, and it can be expressed asthe ratio, LD₅₀/ED₅₀. Pharmaceutical compositions which exhibit largetherapeutic indices are preferred. The data obtained from cell cultureassays and animal studies is used in formulating a range of dosage forhuman use. The dosage contained in such compositions is preferablywithin a range of circulating concentrations that include the ED₅₀ withlittle or no toxicity. The dosage varies within this range dependingupon the dosage form employed, sensitivity of the patient, and the routeof administration. The exact dosage will be determined by thepractitioner, in light of factors related to the subject that requirestreatment. Dosage and administration are adjusted to provide sufficientlevels of the active ingredient or to maintain the desired effect.Factors which can be taken into account include the severity of thedisease state, general health of the subject, age, weight, and gender ofthe subject, diet, time and frequency of administration, drugcombination(s), reaction sensitivities, and tolerance/response totherapy. Long-acting pharmaceutical compositions can be administeredevery 3 to 4 days, every week, or once every two weeks depending on thehalf-life and clearance rate of the particular formulation.

Normal dosage amounts can vary from 0.1 micrograms to 100,000micrograms, up to a total dose of about 1 g, depending upon the route ofadministration. Guidance as to particular dosages and methods ofdelivery is provided in the literature and generally available topractitioners in the art. Those skilled in the art will employ differentformulations for nucleotides than for proteins or their inhibitors.Similarly, delivery of polynucleotides or polypeptides will be specificto particular cells, conditions, locations, etc. If the reagent is asingle-chain antibody, polynucleotides encoding the antibody can beconstructed and introduced into a cell either ex vivo or in vivo usingwell-established techniques including, but not limited to,transferrin-polycation-mediated DNA transfer, transfection with naked orencapsulated nucleic acids, liposome-mediated cellular fusion,intracellular transportation of DNA-coated latex beads, protoplastfusion, viral infection, electroporation, “gene gun”, and DEAE- orcalcium phosphate-mediated transfection.

If the expression product is mRNA, the reagent is preferably anantisense oligonucleotide or a ribozyme. Polynucleotides which expressantisense oligonucleotides or ribozymes can be introduced into cells bya variety of methods, as described above. Preferably, a reagent reducesexpression of 5-HT1F gene or the activity of 5-HT1F by at least about10, preferably about 50, more preferably about 75, 90, or 100% relativeto the absence of the reagent. The effectiveness of the mechanism chosento decrease the level of expression of 5-HT1F gene or the activity of5-HT1F can be assessed using methods well known in the art, such ashybridization of nucleotide probes to 5-HT1F-specific mRNA, quantitativeRT-PCR, immunologic detection of 5-HT1F, or measurement of 5-HT1Factivity.

In any of the embodiments described above, any of the pharmaceuticalcompositions of the invention can be administered in combination withother appropriate therapeutic agents. Selection of the appropriateagents for use in combination therapy can be made by one of ordinaryskill in the art, according to conventional pharmaceutical principles.The combination of therapeutic agents can act synergistically to effectthe treatment or prevention of the various disorders described above.Using this approach, one may be able to achieve therapeutic efficacywith lower dosages of each agent, thus reducing the potential foradverse side effects. Any of the therapeutic methods described above canbe applied to any subject in need of such therapy, including, forexample, mammals such as dogs, cats, cows, horses, rabbits, monkeys, andmost preferably, humans.

Nucleic acid molecules of the invention are those nucleic acid moleculeswhich are contained in a group of nucleic acid molecules consisting of(i) nucleic acid molecules encoding a polypeptide comprising the aminoacid sequence of SEQ ID NO: 2, (ii) nucleic acid molecules comprisingthe sequence of SEQ ID NO: 1, (iii) nucleic acid molecules having thesequence of SEQ ID NO: 1, (iv) nucleic acid molecules the complementarystrand of which hybridizes under stringent conditions to a nucleic acidmolecule of (i), (ii), or (iii); and (v) nucleic acid molecules thesequence of which differs from the sequence of a nucleic acid moleculeof (iii) due to the degeneracy of the genetic code, wherein thepolypeptide encoded by said nucleic acid molecule has 5-HT1F activity.

Polypeptides of the invention are those polypeptides which are containedin a group of polypeptides consisting of (i) polypeptides having thesequence of SEQ ID NO: 2, (ii) polypeptides comprising the sequence ofSEQ ID NO: 2, (iii) polypeptides encoded by nucleic acid molecules ofthe invention and (iv) polypeptides which show at least 99%, 98%, 95%,90%, or 80% homology with a polypeptide of (i), (ii), or (iii), whereinsaid purified polypeptide has 5-HT1F activity.

An object of the invention is a method of screening for therapeuticagents useful in the treatment of a disease comprised in a group ofdiseases consisting of hematological diseases, disorders of theperipheral and central nervous system, gastrointestinal diseases,cardiovascular diseases, cancer, muscle/skeleton disorders, respiratorydiseases and urological diseases in a mammal comprising the steps of (i)contacting a test compound with a 5-HT1F polypeptide, (ii) detectbinding of said test compound to said 5-HT1F polypeptide. E.g.,compounds that bind to the 5-HT1F polypeptide are identified potentialtherapeutic agents for such a disease.

Another object of the invention is a method of screening for therapeuticagents useful in the treatment of a disease comprised in a group ofdiseases consisting of hematological diseases, disorders of theperipheral and central nervous system, gastrointestinal diseases,cardiovascular diseases, cancer, muscle/skeleton disorders, respiratorydiseases and urological diseases in a mammal comprising the steps of (i)determining the activity of a 5-HT1F polypeptide at a certainconcentration of a test compound or in the absence of said testcompound, (ii) determining the activity of said polypeptide at adifferent concentration of said test compound. E.g., compounds that leadto a difference in the activity of the 5-HT1F polypeptide in (i) and(ii) are identified potential therapeutic agents for such a disease.

Another object of the invention is a method of screening for therapeuticagents useful in the treatment of a disease comprised in a group ofdiseases consisting of hematological diseases, disorders of theperipheral and central nervous system, gastrointestinal diseases,cardiovascular diseases, cancer, muscle/skeleton disorders, respiratorydiseases and urological diseases in a mammal comprising the steps of (i)determining the activity of a 5-HT1F polypeptide at a certainconcentration of a test compound, (ii) determining the activity of a5-HT1F polypeptide at the presence of a compound known to be a regulatorof a 5-HT1F polypeptide. E.g., compounds that show similar effects onthe activity of the 5-HT1F polypeptide in (i) as compared to compoundsused in (ii) are identified potential therapeutic agents for such adisease.

Other objects of the invention are methods of the above, wherein thestep of contacting is in or at the surface of a cell.

Other objects of the invention are methods of the above, wherein thecell is in vitro.

Other objects of the invention are methods of the above, wherein thestep of contacting is in a cell-free system.

Other objects of the invention are methods of the above, wherein thepolypeptide is coupled to a detectable label.

Other objects of the invention are methods of the above, wherein thecompound is coupled to a detectable label.

Other objects of the invention are methods of the above, wherein thetest compound displaces a ligand which is first bound to thepolypeptide.

Other objects of the invention are methods of the above, wherein thepolypeptide is attached to a solid support.

Other objects of the invention are methods of the above, wherein thecompound is attached to a solid support.

Another object of the invention is a method of screening for therapeuticagents useful in the treatment of a disease comprised in a group ofdiseases consisting of hematological diseases, disorders of theperipheral and central nervous system, gastrointestinal diseases,cardiovascular diseases, cancer, muscle/skeleton disorders, respiratorydiseases and urological diseases in a mammal comprising the steps of (i)contacting a test compound with a 5-HT1F polynucleotide, (ii) detectbinding of said test compound to said 5-HT1F polynucleotide. Compoundsthat, e.g., bind to the 5HT1F polynucleotide are potential therapeuticagents for the treatment of such diseases.

Another object of the invention is the method of the above, wherein thenucleic acid molecule is RNA.

Another object of the invention is a method of the above, wherein thecontacting step is in or at the surface of a cell.

Another object of the invention is a method of the above, wherein thecontacting step is in a cell-free system.

Another object of the invention is a method of the above, wherein thepolynucleotide is coupled to a detectable label.

Another object of the invention is a method of the above, wherein thetest compound is coupled to a detectable label.

Another object of the invention is a method of diagnosing a diseasecomprised in a group of diseases consisting of hematological diseases,disorders of the peripheral and central nervous system, gastrointestinaldiseases, cardiovascular diseases, cancer, muscle/skeleton disorders,respiratory diseases and urological diseases in a mammal comprising thesteps of (i) determining the amount of a 5-HT1F polynucleotide in asample taken from said mammal, (ii) determining the amount of 5-HT1Fpolynucleotide in healthy and/or diseased mammal. A disease isdiagnosed, e.g., if there is a substantial similarity in the amount of5-HT1F polynucleotide in said test mammal as compared to a diseasedmammal.

Another object of the invention is a pharmaceutical composition for thetreatment of a disease comprised in a group of diseases consisting ofhematological diseases, disorders of the peripheral and central nervoussystem, gastrointestinal diseases, cardiovascular diseases, cancer,muscle/skeleton disorders, respiratory diseases and urological diseasesin a mammal comprising a therapeutic agent which binds to a 5-HT1Fpolypeptide.

Another object of the invention is a pharmaceutical composition for thetreatment of a disease comprised in a group of diseases consisting ofhematological diseases, disorders of the peripheral and central nervoussystem, gastrointestinal diseases, cardiovascular diseases, cancer,muscle/skeleton disorders, respiratory diseases and urological diseasesin a mammal comprising a therapeutic agent which regulates the activityof a 5-HT1F polypeptide.

Another object of the invention is a pharmaceutical composition for thetreatment of a disease comprised in a group of diseases consisting ofhematological diseases, disorders of the peripheral and central nervoussystem, gastrointestinal diseases, cardiovascular diseases, cancer,muscle/skeleton disorders, respiratory diseases and urological diseasesin a mammal comprising a therapeutic agent which regulates the activityof a 5-HT1F polypeptide, wherein said therapeutic agent is (i) a smallmolecule, (ii) an RNA molecule, (iii) an antisense oligonucleotide, (iv)a polypeptide, (v) an antibody, or (vi) a ribozyme.

Another object of the invention is a pharmaceutical composition for thetreatment of a disease comprised in a group of diseases consisting ofhematological diseases, disorders of the peripheral and central nervoussystem, gastrointestinal diseases, cardiovascular diseases, cancer,muscle/skeleton disorders, respiratory diseases and urological diseasesin a mammal comprising a 5-HT1F polynucleotide.

Another object of the invention is a pharmaceutical composition for thetreatment of a disease comprised in a group of diseases consisting ofhematological diseases, disorders of the peripheral and central nervoussystem, gastrointestinal diseases, cardiovascular diseases, cancer,muscle/skeleton disorders, respiratory diseases and urological diseasesin a mammal comprising a 5-HT1F polypeptide.

Another object of the invention is the use of regulators of a 5-HT1F forthe preparation of a pharmaceutical composition for the treatment of adisease comprised in a group of diseases consisting of hematologicaldiseases, disorders of the peripheral and central nervous system,gastrointestinal diseases, cardiovascular diseases, cancer,muscle/skeleton disorders, respiratory diseases and urological diseasesin a mammal.

Another object of the invention is a method for the preparation of apharmaceutical composition useful for the treatment of a diseasecomprised in a group of diseases consisting of hematological diseases,disorders of the peripheral and central nervous system, gastrointestinaldiseases, cardiovascular diseases, cancer, muscle/skeleton disorders,respiratory diseases and urological diseases in a mammal comprising thesteps of (i) identifying a regulator of 5-HT1F, (ii) determining whethersaid regulator ameliorates the symptoms of a disease comprised in agroup of diseases consisting of hematological diseases, disorders of theperipheral and central nervous system, gastrointestinal diseases,cardiovascular diseases, cancer, muscle/skeleton disorders, respiratorydiseases and urological diseases in a mammal; and (iii) combining ofsaid regulator with an acceptable pharmaceutical carrier.

Another object of the invention is the use of a regulator of 5-HT1F forthe regulation of 5-HT1F activity in a mammal having a disease comprisedin a group of diseases consisting of hematological diseases, disordersof the peripheral and central nervous system, gastrointestinal diseases,cardiovascular diseases, cancer, muscle/skeleton disorders, respiratorydiseases and urological diseases.

The examples below are provided to illustrate the subject invention.These examples are provided by way of illustration and are not includedfor the purpose of limiting the invention.

EXAMPLES Example 1 Search for Homologous Sequences in Public SequenceData Bases

The degree of homology can readily be calculated by known methods.Preferred methods to determine homology are designed to give the largestmatch between the sequences tested. Methods to determine homology arecodified in publicly available computer programs such as BestFit,BLASTP, BLASTN, and FASTA. The BLAST programs are publicly availablefrom NCBI and other sources in the internet.

For 5-HT1F the following hits to known sequences were identified byusing the BLAST algorithm [Altschul S F, Madden T L, Schaffer A A, ZhangJ, Zhang Z, Miller W, Lipman D J; Nucleic Acids Res 1997 Sep. 1; 25(17):3389-402] and the following set of parameters: matrix=BLOSUM62 and lowcomplexity filter. The following databases were searched: NCBI(non-redundant database) and DERWENT patent database (Geneseq).

The following hits were found:

>gb|AR080631.1|AR080631 Sequence 8 from patent U.S. Pat. No. 5,968,817,Length 1554, Score=2117 bits (1101), Expect=0.0, Identities=1101/1101(100%)>

>emb|AX548724.1| Sequence 9 from Patent WO02061087, Length=1101,Score=2117 bits (1101), Expect=0.0, Identities=1101/1101 (100%)>

>gb|I58394.1|I158394 Sequence 1 from patent U.S. Pat. No. 5,652,113,Length=1730, Score=2117 bits (1101), Expect=0.0, Identities=1101/1101(100%)>

>gb|I46906.1|I46906 Sequence 1 from patent U.S. Pat. No. 5,639,652,Length=1730, Score=2117 bits (1101), Expect=0.0, Identities=1101/1101(100%)

>gb|AC119733.2| Homo sapiens 3 RP11-159G9 (Roswell Park Cancer InstituteHuman BAC Library) complete sequence, Length=154803, Score=2117 bits(1101), Expect=0.0, Identities=1101/1101 (100%)

>gb|AF498981.1| Homo sapiens 5-hydroxytryptamine receptor 1F (HTR1F)mRNA, complete cds, Length=1101, Score=2117 bits (1101), Expect=0.0,Identities=1101/1101 (100%)>

>ref|NM_(—)000866.1| Homo sapiens 5-hydroxytryptamine (serotonin)receptor IF (HTR1F), mRNA, Length=1101, Score=2117 bits (1101),Expect=0.0, Identities=1101/1101 (100%)

>gb|L04962.1|HUMSRCPT1F Homo sapiens serotonin receptor (HTR1F) gene,complete cds, Length=1141, Score=2117 bits (1101), Expect=0.0,Identities=1101/1101 (100%)

>gb|L5597.1|HUMSEROTON Human serotonin receptor gene, complete cds,Length=1554, Score=2117 bits (1101), Expect=0.0, Identities=1101/1101(100%)

>emb|A74286.1| Sequence 4 from Patent WO9401556, Length=1100, Score=2115bits (1100), Expect=0.0, Identities=1100/1100 (100%)>

>dbj|AB037533.1| Homo sapiens HTR1F gene for 5-hydroxytryptamine(serotonin) receptor IF, partial cds, Length=1125, Score=2107 bits(1096), Expect=0.0, Identities=1096/1096 (100%)

>emb|AX280809.1| Sequence 432 from Patent WO0177172, Length=1101,Score=2100 bits (1092), Expect=0.0, Identities=1098/1101 (99%)

>dbj|AB037534.1| Pan troglodytes HTR1F gene for 5-hydroxytryptamine(serotonin), receptor 1F, partial cds, Length=1125, Score=2094 bits(1089), Expect=0.0, Identities=1093/1096 (99%)

>dbj|AB037535.1| Gorilla gorilla HTR1F gene for 5-hydroxytryptamine(serotonin), receptor IF, partial cds, Length=1125, Score=2073 bits(1078), Expect=0.0, Identities=1090/1096 (99%)

Example 2 Expression Profiling

Total cellular RNA was isolated from cells by one of two standardmethods: 1) guanidine isothiocyanate/Cesium chloride density gradientcentrifugation [Kellogg, (1990)]; or with the Tri-Reagent protocolaccording to the manufacturer's specifications (Molecular ResearchCenter, Inc., Cincinatti, Ohio). Total RNA prepared by the Tri-reagentprotocol was treated with DNAse I to remove genomic DNA contamination.

For relative quantitation of the mRNA distribution of 5-HT1F, total RNAfrom each cell or tissue source was first reverse transcribed. 85 μg oftotal RNA was reverse transcribed using 1 μmole random hexamer primers,0.5 mM each of dATP, dCTP, dGTP and dTTP (Qiagen. Hilden, Germany), 3000U RnaseQut (Invitrogen, Groningen, Netherlands) in a final volume of 680μl. The first strand synthesis buffer and Omniscript reversetranscriptase (2 u/μl) were from (Qiagen, Hilden, Germany). The reactionwas incubated at 37° C. for 90 minutes and cooled on ice. The volume wasadjusted to 6800 μl with water, yielding a final concentration of 12.5ng/μl of starting RNA.

For relative quantitation of the distribution of 5-HT1F mRNA in cellsand tissues the Applied Biosystems 7900 HT Sequence Detection system orBiorad iCycler was used according to the manufacturer's specificationsand protocols. PCR reactions were set up to quantitate 5-HT1F and thehousekeeping genes HPRT (hypoxanthine phosphoribosyltransferase), GAPDH(glyceraldehyde-3-phosphate dehydrogenase), β-actin, and others. Forwardand reverse primers and probes for 5-HT1F were designed using the PerkinElmer ABI Primer Express™ software and were synthesized by TibMolBiol(Berlin, Germany). The 5-HT1F forward primer sequence was: Primer1 (SEQID NO: 3). The 5-HT1F reverse primer sequence was Primer2 (SEQ ID NO:4). Probe1 (SEQ ID NO: 5), labelled with FAM (carboxyfluoresceinsuccinimidyl ester) as the reporter dye and TAMRA(carboxytetramethylrhodamine) as the quencher, is used as a probe for5-HT1F. The following reagents were prepared in a total of 25 μl:1×TaqMan buffer A, 5.5 mM MgCl₂, 200 nM of DATP, dCTP, dGTP, and dUTP,0.025 U/μl AmpliTaq Gold™, 0.01 U/μl AmpErase and Probe1 (SEQ ID NO: 4),5-HT1F forward and reverse primers each at 200 nM, 200 nM 5-HT1FFAM/TAMRA-labelled probe, and 5 μl of template cDNA. Thermal cyclingparameters were 2 min at 50° C., followed by 10 min at 95° C., followedby 40 cycles of melting at 95° C. for 15 sec and annealing/extending at60° C. for 1 min.

Calculation of Corrected CT Values

The CT (threshold cycle) value is calculated as described in the“Quantitative determination of nucleic acids” section. The CF-value(factor for threshold cycle correction) is calculated as follows:

-   1. PCR reactions were set up to quantitate the housekeeping genes    (RKG) for each cDNA sample.-   2. CT_(HKG)-values (threshold cycle for housekeeping gene) were    calculated as described in the “Quantitative determination of    nucleic acids” section.-   3. CT_(HKG)-mean values (CT mean value of all HKG tested on one    cDNAs) of all HKG for each cDNA are calculated (n=number of HKG):    CT _(HKG-n)-mean value=(CT _(HKG1)-value+CT _(HKG2)-value+ . . .+CT    _(HKG-n)-value)/n-   4. CT_(pannel) mean value (CT mean value of all HKG in all tested    cDNAs)=    (CT_(HKG1)-mean value+CT_(HKG2)-mean value+ . . . +CT_(HKG-y)-mean    value)/y (y=number of cDNAs)-   5. CF_(cDNA-n) (correction factor for cDNA n)=CT_(pannel)-mean value    CT_(HKG-n)-mean value-   6. CT_(cDNA-n) (CT value of the tested gene for the cDNA    n)+CF_(cDNA-n) (correction factor for cDNA n)=CT_(cor-cDNA-n)    (corrected CT value for a gene on cDNA n)    Calculation of Relative Expression    Definition: highest CT_(cor-cDNA-n)≠40 is defined as CT_(cor-DNA)    [high]    Relative Expression=2^((CTor-cDNA[high]−CTcor-cDNA-n))    Tissues

The expression of 5-HT1F was investigated in the tissues listed in table1.

Expression Profile

The results of the the mRNA-quantification (expression profiling) isshown in Table 1. TABLE 1 Relative expression of 5-HT1F in various humantissues Tissue Relative Expression fetal heart 38 heart 239 pericardium541 heart atrium (right) 526 heart atrium (left) 182 heart ventricle(left) 191 heart ventricle (right) 1 heart apex 771 Purkinje fibers 1113interventricular septum 134 fetal aorta 25 aorta 19 aorta sclerotic 194artery 105 coronary artery 20 coronary artery sclerotic 150 pulmonaryartery 55 carotid artery 15 mesenteric artery 1 vein 80 pulmonic valve2385 coronary artery smooth muscle primary cells 516 aortic smoothmuscle cells 74 pulmonary artery smooth muscle cells 690 aortic endothelcells 89 coronary artery endothel cells 704 HUVEC cells 58 pulmonaryartery endothel cells 112 iliac artery endothel cells 296 skin 516adrenal gland 118 thyroid 194 thyroid tumor 873 pancreas 449 pancreasliver cirrhosis 1 esophagus 1 esophagus tumor 96 stomach 139 stomachtumor 576 colon 108 colon tumor 224 small intestine 187 ileum 478 ileumtumor 152 ileum chronic inflammation 1 rectum 2048 salivary gland 37fetal liver 399 liver 51 liver liver cirrhosis 2937 liver lupus disease17 liver tumor 76 HEP G2 cells 501 leukocytes (peripheral blood) 79Jurkat (T-cells) 553 bone marrow 229 erythrocytes 592 lymphnode 7 thymus484 thrombocytes 491 bone marrow stromal cells 239 bone marrow CD71+cells 249 bone marrow CD33+ cells 724 bone marrow CD34+ cells 1060 bonemarrow CD15+ cells 699 cord blood CD71+ cells 491 cord blood CD34+ cells4124 neutrophils cord blood 739 neutrophils peripheral blood 849 spleen1687 spleen liver cirrhosis 179 skeletal muscle 428 cartilage 5405 boneconnective tissue 969 adipose 709 fetal brain 592 brain 2020 Alzheimerbrain 3956 cerebellum 516 Alzheimer brain cerebellum 19083 cerebellum(right) 2957 cerebellum (left) 2452 cerebral cortex 7033 Alzheimercerebral cortex 3148 frontal lobe 11347 Alzheimer brain frontal lobe9090 occipital lobe 2272 parietal lobe 3541 temporal lobe 1380postcentral gyrus 461 vermis cerebelli 690 pons 505 substantia nigra3591 caudatum 6562 cerebral meninges 61 cerebral peduncles 53 corpuscallosum 1820 nucleus accumbens 1278 putamen 699 hippocampus 5078thalamus 324 posteroventral thalamus 2916 dorsalmedial thalamus 3929hypothalamus 2876 dorsal root ganglia 4 spinal cord 626 spinal cord(ventral horn) 2702 spinal cord (dorsal horn) 4360 neuroblastoma SK-N-MCcells 237 neuroblastoma SH-SY5Y cells 98 neuroblastoma IMR32 cells 468glial tumor H4 cells 150 HEK CNS + APP 605 neural progenitor cells 596astrocytes 1201 retina 1370 fetal lung 237 fetal lung fibroblast IMR-90cells 6 fetal lung fibroblast MRC-5 cells 3 lung 180 lung right upperlobe 88 lung right mid lobe 468 lung right lower lobe 505 lung lupusdisease 23 lung tumor 704 lung COPD 96 trachea 396 primary bronchia 1075secondary bronchia 1872 bronchial epithelial cells 1885 bronchial smoothmuscle cells 776 small airway epithelial cells 236 cervix 329 testis 399HeLa cells (cervix tumor) 1 placenta 685 uterus 820 uterus tumor 322ovary 434 ovary tumor 1046 breast 626 breast tumor 809 MDA MB 231 cells(breast tumor) 217 mammary gland 360 prostate 357 prostate BPH 44prostate tumor 8079 bladder 74 ureter 355 penis 1965 corpus cavernosum584 fetal kidney 2487 kidney 251 kidney tumor 792 renal epithelial cells867 HEK 293 cells 434

Example 3 Antisense Analysis

Knowledge of the correct, complete cDNA sequence coding for 5-HT1Fenables its use as a tool for antisense technology in the investigationof gene function. Oligonucleotides, cDNA or genomic fragments comprisingthe antisense strand of a polynucleotide coding for 5-HT1F are usedeither in vitro or in vivo to inhibit translation of the mRNA. Suchtechnology is now well known in the art, and antisense molecules can bedesigned at various locations along the nucleotide sequences. Bytreatment of cells or whole test animals with such antisense sequences,the gene of interest is effectively turned off. Frequently, the functionof the gene is ascertained by observing behavior at the intracellular,cellular, tissue or organismal level (e.g., lethality, loss ofdifferentiated function, changes in morphology, etc.).

In addition to using sequences constructed to interrupt transcription ofa particular open reading frame, modifications of gene expression isobtained by designing antisense sequences to intron regions,promoter/enhancer elements, or even to transacting regulatory genes.

Example 4 Expression of 5-HT1F

Expression of 5-HT1F is accomplished by subcloning the cDNAs intoappropriate expression vectors and transfecting the vectors intoexpression hosts such as, e.g., E. coli. In a particular case, thevector is engineered such that it contains a promoter forβ-galactosidase, upstream of the cloning site, followed by sequencecontaining the amino-terminal Methionine and the subsequent sevenresidues of β-galactosidase. Immediately following these eight residuesis an engineered bacteriophage promoter useful for artificial primingand transcription and for providing a number of unique endonucleaserestriction sites for cloning.

Induction of the isolated, transfected bacterial strain withIsopropyl-β-D-thiogalactopyranoside (IPTG) using standard methodsproduces a fusion protein corresponding to the first seven residues ofβ-galactosidase, about 15 residues of “linker”, and the peptide encodedwithin the cDNA. Since cDNA clone inserts are generated by anessentially random process, there is probability of 33% that theincluded cDNA will lie in the correct reading frame for propertranslation. If the cDNA is not in the proper reading frame, it isobtained by deletion or insertion of the appropriate number of basesusing well known methods including in vitro mutagenesis, digestion withexonuclease III or mung bean nuclease, or the inclusion of anoligonucleotide linker of appropriate length.

The 5-HT1F cDNA is shuttled into other vectors known to be useful forexpression of proteins in specific hosts. Oligonucleotide primerscontaining cloning sites as well as a segment of DNA (about 25 bases)sufficient to hybridize to stretches at both ends of the target cDNA issynthesized chemically by standard methods. These primers are then usedto amplify the desired gene segment by PCR. The resulting gene segmentis digested with appropriate restriction enzymes under standardconditions and isolated by gel electrophoresis. Alternately, similargene segments are produced by digestion of the cDNA with appropriaterestriction enzymes. Using appropriate primers, segments of codingsequence from more than one gene are ligated together and cloned inappropriate vectors. It is possible to optimize expression byconstruction of such chimeric sequences.

Suitable expression hosts for such chimeric molecules include, but arenot limited to, mammalian cells such as Chinese Hamster Ovary (CHO) andhuman 293 cells., insect cells such as Sf9 cells, yeast cells such asSaccharomyces cerevisiae and bacterial cells such as E. coli. For eachof these cell systems, a useful expression vector also includes anorigin of replication to allow propagation in bacteria, and a selectablemarker such as the β-lactamase antibiotic resistance gene to allowplasmid selection in bacteria. In addition, the vector may include asecond selectable marker such as the neomycin phosphotransferase gene toallow selection in transfected eukaryotic host cells. Vectors for use ineukaryotic expression hosts require RNA processing elements such as 3′polyadenylation sequences if such are not part of the cDNA of interest.

Additionally, the vector contains promoters or enhancers which increasegene expression. Such promoters are host specific and include MMTV,SV40, and metallothionine promoters for CHO cells; trp, lac, tac and T7promoters for bacterial hosts; and alpha factor, alcohol oxidase and PGHpromoters for yeast. Transcription enhancers, such as the rous sarcomavirus enhancer, are used in mammalian host cells. Once homogeneouscultures of recombinant cells are obtained through standard culturemethods, large quantities of recombinantly produced 5-HT1F are recoveredfrom the conditioned medium and analyzed using chromatographic methodsknown in the art. For example, 5-HT1F can be cloned into the expressionvector pcDNA3, as exemplified herein. This product can be used totransform, for example, HEK293 or COS by methodology standard in theart. Specifically, for example, using Lipofectamine (Gibco BRL catologno. 18324-020) mediated gene transfer.

Example 5 Isolation of Recombinant 5-HT1F

5-HT1F is expressed as a chimeric protein with one or more additionalpolypeptide domains added to facilitate protein purification. Suchpurification facilitating domains include, but are not limited to, metalchelating peptides such as histidine-tryptophan modules that allowpurification on immobilized metals [Appa Rao, 1997] and the domainutilized in the FLAGS extension/affinity purification system (ImmunexCorp., Seattle, Wash.). The inclusion of a cleavable linker sequencesuch as Factor Xa or enterokinase (Invitrogen, Groningen, TheNetherlands) between the purification domain and the 5-HT1F sequence isuseful to facilitate expression of 5-HT1F.

Example 6 Testing of Chimeric GPCRs

Functional chimeric GPCRs are constructed by combining the extracellularreceptive sequences of a new isoform with the transmembrane andintracellular segments of a known isoform for test purposes. Thisconcept was demonstrated by Kobilka et al. (1988), Science240:1310-1316) who created a series of chimeric α2-β2 adrenergicreceptors (AR) by inserting progressively greater amounts of α2-ARtransmembrane sequence into β2-AR. The binding activity of knownagonists changed as the molecule shifted from having more α2 than β2conformation, and intermediate constructs demonstrated mixedspecificity. The specificity for binding antagonists, however,correlated with the source of the domain VII. The importance of T7Gdomain VII for ligand recognition was also found in chimeras utilizingtwo yeast α-factor receptors and is significant because-the yeastreceptors are classified as miscellaneous receptors. Thus, functionalrole of specific domains appears to be preserved throughout the GPCRfamily regardless of category.

In parallel fashion, internal segments or cytoplasmic domains from aparticular isoform are exchanged with the analogous domains of a knownGPCRs and used to identify the structural determinants responsible forcoupling the receptors to trimeric G-proteins. A chimeric receptor inwhich domains V, VI, and the intracellular connecting loop from β2-ARwere substituted into α2-AR was shown to bind ligands with α2-ARspecificity, but to stimulate adenylate cyclase in the manner of β2-AR.This demonstrates that for adrenergic-type receptors, G-proteinrecognition is present in domains V and VI and their connecting loop.The opposite situation was predicted and observed for a chimera in whichthe V->VI loop from α1-AR replaced the corresponding domain on β2-AR andthe resulting receptor bound ligands with β2-AR specificity andactivated G-protein-mediated phosphatidylinositol turnover in the α1-ARmanner. Finally, chimeras constructed from muscarinic receptors alsodemonstrated that V->VI loop is the major determinant for specificity ofG-protein activity. Chimeric or modified GPCRs containing substitutionsin the extracellular and transmembrane regions have shown that theseportions of the receptor determine ligand binding specificity. Forexample, two Serine residues conserved in domain V of all adrenergic andD catecholainine GPCRs are necessary for potent agonist activity. Theseserines are believed to form hydrogen bonds with the catechol moiety ofthe agonists within the GPCR binding site. Similarly, an Asp residuepresent in domain III of all GPCRs which bind biogenic amines isbelieved to form an ion pair with the ligand amine group in the GPCRbinding site.

Functional, cloned GPCRs are expressed in heterologous expressionsystems and their biological activity assessed. One heterologous systemintroduces genes for a mammalian GPCR and a mammalian G-protein intoyeast cells. The GPCR is shown to have appropriate ligand specificityand affinity and trigger appropriate biological activation (growtharrest and morphological changes) of the yeast cells.

An alternate procedure for testing chimeric receptors is based on theprocedure utilizing the purinergic receptor (P₂u). Function is easilytested in cultured K562 human leukemia cells because these cells lackP₂u receptors. K562 cells are transfected with expression vectorscontaining either normal or chimeric P₂u and loaded with fura-a,fluorescent probe for Ca⁺⁺. Activation of properly assembled andfunctional P₂u receptors with extracellular UTP or ATP mobilizesintracellular Ca⁺⁺ which reacts with fura-a and is measuredspectrofluorometrically.

As with the GPCRs above, chimeric genes are created by combiningsequences for extracellular receptive segments of any new GPCRpolypeptide with the nucleotides for the transmembrane and intracellularsegments of the known P₂u molecule. Bathing the transfected K562 cellsin microwells containing appropriate ligands triggers binding andfluorescent activity defining effectors of the GPCR molecule. Onceligand and function are established, the P₂u system is useful fordefining antagonists or inhibitors which block binding and prevent suchfluorescent reactions.

Example 7 Production of 5-HT1F Specific Antibodies

Two approaches are utilized to raise antibodies to 5-HT1F, and eachapproach is useful for generating either polyclonal or monoclonalantibodies. In one approach, denatured protein from reverse phase HPLCseparation is obtained in quantities up to 75 mg. This denatured proteinis used to immunize mice or rabbits using standard protocols; about 100μg are adequate for immunization of a mouse, while up to 1 mg might beused to immunize a rabbit. For identifying mouse hybridomas, thedenatured protein is radioiodinated and used to screen potential murineB-cell hybridomas for those which produce antibody. This procedurerequires only small quantities of protein, such that 20 mg is sufficientfor labeling and screening of several thousand clones.

In the second approach, the amino acid sequence of an appropriate 5-HT1Fdomain, as deduced from translation of the cDNA, is analyzed todetermine regions of high antigenicity. Oligopeptides comprisingappropriate hydrophilic regions are synthesized and used in suitableimmunization protocols to raise antibodies. The optimal amino acidsequences for immunization are usually at the C-terminus, the N-terminusand those intervening, hydrophilic regions of the polypeptide which arelikely to be exposed to the external environment when the protein is inits natural conformation.

Typically, selected peptides, about 15 residues in length, aresynthesized using an Applied Biosystems Peptide Synthesizer Model 431Ausing fmoc-chemistry and coupled to keyhole limpet hemocyanin (KLH;Sigma, St. Louis, Mo.) by reaction withM-maleimidobenzoyl-N-hydroxysuccinimde ester, MBS. If necessary, acysteine is introduced at the N-terminus of the peptide to permitcoupling to KLH. Rabbits are immunized with the peptide-KLH complex incomplete Freund's adjuvant. The resulting antisera are tested forantipeptide activity by binding the peptide to plastic, blocking with 1%bovine serum albumin, reacting with antisera, washing and reacting withlabeled (radioactive or fluorescent), affinity purified, specific goatanti-rabbit IgG.

Hybridomas are prepared and screened using standard techniques.Hybridomas of interest are detected by screening with labeled 5-HT1F toidentify those fusions producing the monoclonal antibody with thedesired specificity. In a typical protocol, wells of plates (FAST;Becton-Dickinson, Palo Alto, Calif.) are coated during incubation withaffinity purified, specific rabbit anti-mouse (or suitable antispecies 1g) antibodies at 10 ng/ml. The coated wells are blocked with 1% bovineserum albumin, (BSA), washed and incubated with supernatants fromhybridomas. After washing the wells are incubated with labeled 5-HT1F at1 mg/ml. Supernatants with specific antibodies bind more labeled 5-HT1Fthan is detectable in the background. Then clones producing specificantibodies are expanded and subjected to two cycles of cloning atlimiting dilution. Cloned hybridomas are injected into pristane-treatedmice to produce ascites, and monoclonal antibody is purified from mouseascitic fluid by affinity chromatography on Protein A. Monoclonalantibodies with affinities of at least

10⁸M⁻¹, preferably 10⁹ to 10¹⁰ M⁻¹ or stronger, are typically made bystandard procedures.

Example 8 Diagnostic Test Using 5-HT1F Specific Antibodies

Particular 5-HT1F antibodies are useful for investigating signaltransduction and the diagnosis of infectious or hereditary conditionswhich are characterized by differences in the amount or distribution of5-HT1F or downstream products of an active signaling cascade.

Diagnostic tests for 5-HT1F include methods utilizing antibody and alabel to detect 5-HT1F in human body fluids, membranes, cells, tissuesor extracts of such. The polypeptides and antibodies of the presentinvention are used with or without modification. Frequently, thepolypeptides and antibodies are labeled by joining them, eithercovalently or noncovalently, with a substance which provides for adetectable signal. A wide variety of labels and conjugation techniquesare known and have been reported extensively in both the scientific andpatent literature. Suitable labels include radionuclides, enzymes,substrates, cofactors, inhibitors, fluorescent agents, chemiluminescentagents, chromogenic agents, magnetic particles and the like.

A variety of protocols for measuring soluble or membrane-bound 5-HT1F,using either polyclonal or monoclonal antibodies specific for theprotein, are known in the art. Examples include enzyme-linkedimmunosorbent assay (ELISA), radioimmunoassay (RIA) and fluorescentactivated cell sorting (FACS). A two-site monoclonal-based immunoassayutilizing monoclonal antibodies reactive to two non-interfering epitopeson 5-HT1F is preferred, but a competitive binding assay may be employed.

Example 9 Purification of Native 5-HT1F Using Specific Antibodies

Native or recombinant 5-HT1F is purified by immunoaffinitychromatography using antibodies specific for 5-HT1F. In general, animmunoaffinity column is constructed by covalently coupling the anti-TRHantibody to an activated chromatographic resin.

Polyclonal immunoglobulins are prepared from immune sera either byprecipitation with ammonium sulfate or by purification on immobilizedProtein A (Pharmacia LKB Biotechnology, Piscataway N.J.). Likewise,monoclonal antibodies are prepared from mouse ascites fluid by ammoniumsulfate precipitation or chromatography on immobilized Protein A.Partially purified immunoglobulin is covalently attached to achromatographic resin such as CnBr-activated Sepharose (Pharmacia LKBBiotechnology). The antibody is coupled to the resin, the resin isblocked, and the derivative resin is washed according to themanufacturer's instructions.

Such immunoaffinity columns are utilized in the purification of 5-HT1Fby preparing a fraction from cells containing 5-HT1F in a soluble form.This preparation is derived by solubilization of whole cells or of asubcellular fraction obtained via differential centrifugation (with orwithout addition of detergent) or by other methods well known in theart. Alternatively, soluble 5-HT1F containing a signal sequence issecreted in useful quantity into the medium in which the cells aregrown.

A soluble 5-HT1F-containing preparation is passed over theimmunoaffinity column, and the column is washed under conditions thatallow the preferential absorbance of 5-HT1F (e.g., high ionic strengthbuffers in the presence of detergent). Then, the column is eluted underconditions that disrupt antibody/protein binding (e.g., a buffer of pH2-3 or a high concentration of a chaotrope such as urea or thiocyanateion), and 5-HT1F is collected.

Example 10 Drug Screening

This invention is particularly useful for screening therapeuticcompounds by using 5-HT1F or binding fragments thereof in any of avariety of drug screening techniques. As 5-HT1F is a G protein coupledreceptor any of the methods commonly used in the art may potentially beused to identify 5-HT1F ligands. For example, the activity of a Gprotein coupled receptor such as 5-HT1F can be measured using any of avariety of appropriate functional assays in which activation of thereceptor results in an observable change in the level of some secondmessenger system, such as adenylate cyclase, guanylylcyclase, calciummobilization, or inositol phospholipid hydrolysis. Alternatively, thepolypeptide or fragment employed in such a test is either free insolution, affixed to a solid support, borne on a cell surface or locatedintracellularly. One method of drug screening utilizes eukaryotic orprokaryotic host cells which are stably transformed with recombinantnucleic acids expressing the polypeptide or fragment. Drugs are screenedagainst such transformed cells in competitive binding assays. Suchcells, either in viable or fixed form, are used for standard bindingassays.

Measured, for example, is the formation of complexes between 5-HT1F andthe agent being tested. Alternatively, one examines the diminution incomplex formation between 5-HT1F and a ligand caused by the agent beingtested.

Thus, the present invention provides methods of screening for drugcanditates, drugs, or any other agents which affect signal transduction.These methods, well known in the art, comprise contacting such an agentwith 5-HT1F polypeptide or a fragment thereof and assaying (i) for thepresence of a complex between the agent and 5-HT1F polypeptide orfragment, or (ii) for the presence of a complex between 5-HT1Fpolypeptide or fragment and the cell. In such competitive bindingassays, the 5-HT1F polypeptide or fragment is typically labeled. Aftersuitable incubation, free 5-HT1F polypeptide or fragment is separatedfrom that present in bound form, and the amount of free or uncomplexedlabel is a measure of the ability of the particular agent to bind to5-HT1F or to interfere with the 5-HT1F-agent complex.

Another technique for drug screening provides high throughput screeningfor compounds having suitable binding affinity to 5-HT1F polypeptides.Briefly stated, large numbers of different small peptide test compoundsare synthesized on a solid substrate, such as plastic pins or some othersurface. The peptide test compounds are reacted with 5-HT1F polypeptideand washed. Bound 5-HT1F polypeptide is then detected by methods wellknown in the art. Purified 5-HT1F are also coated directly onto platesfor use in the aforementioned drug screening techniques. In addition,non-neutralizing antibodies are used to capture the peptide andimmobilize it on the solid support.

This invention also contemplates the use of competitive drug screeningassays m which neutralizing antibodies capable of binding 5-HT1Fspecifically compete with a test compound for binding to 5-HT1Fpolypeptides or fragments thereof. In this manner, the antibodies areused to detect the presence of any peptide which shares one or moreantigenic determinants with 5-HT1F.

Example 11 Rational Drug Design

The goal of rational drug design is to produce structural analogs ofbiologically active polypeptides of interest or of small molecules withwhich they interact, agonists, antagonists, or inhibitors. Any of theseexamples are used to fashion drugs which are more active or stable formsof the polypeptide or which enhance or interfere with the function of apolypeptide in vivo.

In one approach, the three-dimensional structure of a protein ofinterest, or of a protein-inhibitor complex, is determined by x-raycrystallography, by computer modeling or, most typically, by acombination of the two approaches. Both the shape and charges of thepolypeptide must be ascertained to elucidate the structure and todetermine active site(s) of the molecule. Less often, useful informationregarding the structure of a polypeptide is gained by modeling based onthe structure of homologous proteins. In both cases, relevant structuralinformation is used to design efficient inhibitors. Useful examples ofrational drug design include molecules which have improved activity orstability or which act as inhibitors, agonists, or antagonists of nativepeptides.

It is also possible to isolate a target-specific antibody, selected byfunctional assay, as described above, and then to solve its crystalstructure. This approach, in principle, yields a pharmacore upon whichsubsequent drug design is based. It is possible to bypass proteincrystallography altogether by generating anti-idiotypic antibodies(anti-ids) to a functional, pharmacologically active antibody. As amirror image of a mirror image, the binding site of the anti-ids isexpected to be an analog of the original receptor. The anti-id is thenused to identity and isolate peptides from banks of chemically orbiologically produced peptides. The isolated peptides then act as thepharmacore.

By virtue of the present invention, sufficient amount of polypeptide aremade available to perform such analytical studies as X-raycrystallography. In addition, knowledge of the 5-HT1F amino acidsequence provided herein provides guidance to those employing computermodeling techniques in place of or in addition to x-ray crystallography.

Example 12 Identification of Other Members of the Signal TransductionComplex

The inventive purified 5-HT1F is a research tool for identification,characterization and purification of interacting G or other signaltransduction pathway proteins. Radioactive labels are incorporated intoa selected 5-HT1F domain by various methods known in the art and used invitro to capture interacting molecules. A preferred method involveslabeling the primary amino groups in 5-HT1F with ¹²⁵I Bolton-Hunterreagent. This reagent has been used to label various molecules withoutconcomitant loss of biological activity.

Labeled 5-HT1F is useful as a reagent for the purification of moleculeswith which it interacts. In one embodiment of affinity purification,membrane-bound 5-HT1F is covalently coupled to a chromatography column.Cell-free extract derived from synovial cells or putative target cellsis passed over the column, and molecules with appropriate affinity bindto 5-HT1F. 5-HT1F-complex is recovered from the column, and the5-HT1F-binding ligand disassociated and subjected to N-terminal proteinsequencing. The amino acid sequence information is then used to identifythe captured molecule or to design degenerate oligonucleotide probes forcloning the relevant gene from an appropriate cDNA library.

In an alternate method, antibodies are raised against 5-HT1F,specifically monoclonal antibodies. The monoclonal antibodies arescreened to identify those which inhibit the binding of labeled 5-HT1F.These monoclonal antibodies are then used therapeutically.

Example 13 Use and Administration of Antibodies, Inhibitors, orAntagonists

Antibodies, inhibitors, or antagonists of 5-HT1F or other treatments andcompunds that are limiters of signal transduction (LSTs), providedifferent effects when administered therapeutically. LSTs are formulatedin a nontoxic, inert, pharmaceutically acceptable aqueous carrier mediumpreferably at a pH of about 5 to 8, more preferably 6 to 8, although pHmay vary according to the characteristics of the antibody, inhibitor, orantagonist being formulated and the condition to be treated.Characteristics of LSTs include solubility of the molecule, itshalf-life and antigenicity/immunogenicity. These and othercharacteristics aid in defining an effective carrier. Native humanproteins are preferred as LSTs, but organic or synthetic moleculesresulting from drug screens are equally effective in particularsituations.

LSTs are delivered by known routes of administration including but notlimited to topical creams and gels; transmucosal spray and aerosol;transdermal patch and bandage; injectable, intravenous and lavageformulations; and orally administered liquids and pills particularlyformulated to resist stomach acid and enzymes. The particularformulation, exact dosage, and route of administration is determined bythe attending physician and varies according to each specific situation.

Such determinations are made by considering multiple variables such asthe condition to be treated, the LST to be administered, and thepharmacokinetic profile of a particular LST. Additional factors whichare taken into account include severity of the disease state, patient'sage, weight, gender and diet, time and frequency of LST administration,possible combination with other drugs, reaction sensitivities, andtolerance/response to therapy. Long acting LST formulations might beadministered every 3 to 4 days, every week, or once every two weeksdepending on half-life and clearance rate of the particular LST.

Normal dosage amounts vary from 0.1 to 10⁵ μg, up to a total dose ofabout 1 g, depending upon the route of administration. Guidance as toparticular dosages and methods of delivery is provided in theliterature; see U.S. Pat. No. 4,657,760; 5,206,344; or 5,225,212. Thoseskilled in the art employ different formulations for different LSTs.Administration to cells such as nerve cells necessitates delivery in amanner different from that to other cells such as vascular endothelialcells.

It is contemplated that abnormal signal transduction, trauma, ordiseases which trigger 5-HT1F activity are treatable with LSTs. Theseconditions or diseases are specifically diagnosed by the tests discussedabove, and such testing should be performed in suspected cases of viral,bacterial or fungal infections, allergic responses, mechanical injuryassociated with trauma, hereditary diseases, lymphoma or carcinoma, orother conditions which activate the genes of lymphoid or neuronaltissues.

Example 14 Production of Non-Human Transgenic Animals

Animal model systems which elucidate the physiological and behavioralroles of the 5-HT1F are produced by creating nonhuman transgenic animalsin which the activity of the 5-HT1F is either increased or decreased, orthe amino acid sequence of the expressed 5-HT1F is altered, by a varietyof techniques. Examples of these techniques include, but are not limitedto: 1) Insertion of normal or mutant versions of DNA encoding a 5-HT1F,by microinjection, electroporation, retroviral transfection or othermeans well known to those skilled in the art, into appropriatelyfertilized embryos in order to produce a transgenic animal or 2)homologous recombination of mutant or normal, human or animal versionsof these genes with the native gene locus in transgenic animals to alterthe regulation of expression or the structure of these 5-HT1F sequences.The technique of homologous recombination is well known in the art. Itreplaces the native gene with the inserted gene and hence is useful forproducing an animal that cannot express native 5-HT1Fs but does express,for example, an inserted mutant 5-HT1F, which has replaced the native5-HT1F in the animal's genome by recombination, resulting inunderexpression of the transporter. Microinjection adds genes to thegenome, but does not remove them, and the technique is useful forproducing an animal which expresses its own and added 5-HT1F, resultingin overexpression of the 5-HT1F.

One means available for producing a transgenic animal, with a mouse asan example, is as follows: Female mice are mated, and the resultingfertilized eggs are dissected out of their oviducts. The eggs are storedin an appropriate medium such as cesium-chloride M2 medium. DNA or cDNAencoding 5-HT1F is purified from a vector by methods well known to theone skilled in the art. Inducible promoters may be fused with the codingregion of the DNA to provide an experimental means to regulateexpression of the transgene. Alternatively or in addition, tissuespecific regulatory elements may be fused with the coding region topermit tissue-specific expression of the transgene. The DNA, in anappropriately buffered solution, is put into a microinjection needle(which may be made from capillary tubing using a piper puller) and theegg to be injected is put in a depression slide. The needle is insertedinto the pronucleus of the egg, and the DNA solution is injected. Theinjected egg is then transferred into the oviduct of a pseudopregnantmouse which is a mouse stimulated by the appropriate hormones in orderto maintain false pregnancy, where it proceeds to the uterus, implants,and develops to term. As noted above, microinjection is not the onlymethod for inserting DNA into the egg but is used here only forexemplary purposes.

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1. A method of screening for therapeutic agents useful in the treatmentof a disease selected from hematological diseases, disorders of theperipheral and central nervous system, gastrointestinal diseases,cardiovascular diseases, cancer, muscle/skeleton disorders, respiratorydiseases and urological diseases in a mammal comprising the steps of i)contacting a test compound with a 5-HT1F polypeptide, ii) detectingbinding of said test compound to said 5-HT1F polypeptide.
 2. A method ofscreening for therapeutic agents useful in the treatment of a diseaseselected from hematological diseases, disorders of the peripheral andcentral nervous system, gastrointestinal diseases, cardiovasculardiseases, cancer, muscle/skeleton disorders, respiratory diseases andurological diseases in a mammal comprising the steps of i) determiningthe activity of a 5-HT1F polypeptide at a certain concentration of atest compound or in the absence of said test compound, ii) determiningthe activity of said polypeptide at a different concentration of saidtest compound.
 3. A method of screening for therapeutic agents useful inthe treatment of a disease selected from hematological diseases,disorders of the peripheral and central nervous system, gastrointestinaldiseases, cardiovascular diseases, cancer, muscle/skeleton disorders,respiratory diseases and urological diseases in a mammal comprising thesteps of i) determining the activity of a 5-HT1F polypeptide at acertain concentration of a test compound, ii) determining the activityof a 5-HT1F polypeptide at the presence of a compound known to be aregulator of a 5-HT1F polypeptide.
 4. The method of claim 1, wherein thestep of contacting is in or at the surface of a cell.
 5. The method ofclaim 1, wherein the cell is in vitro.
 6. The method of claim 1, whereinthe step of contacting is in a cell-free system.
 7. The method of claim1, wherein the polypeptide is coupled to a detectable label.
 8. Themethod of claim 1, wherein the compound is coupled to a detectablelabel.
 9. The method of claim 1, wherein the test compound displaces aligand which is first bound to the polypeptide.
 10. The method of claim1, wherein the polypeptide is attached to a solid support.
 11. Themethod of claim 1, wherein the compound is attached to a solid support.12. A method of screening for therapeutic agents useful in the treatmentof a disease selected from hematological diseases, disorders of theperipheral and central nervous system, gastrointestinal diseases,cardiovascular diseases, cancer, muscle/skeleton disorders, respiratorydiseases and urological diseases in a mammal comprising the steps of i)contacting a test compound with a 5-HT1F polynucleotide, ii) detectingbinding of said test compound to said 5-HT1F polynucleotide.
 13. Themethod of claim 12 wherein the nucleic acid molecule is RNA.
 14. Themethod of claim 12 wherein the contacting step is in or at the surfaceof a cell.
 15. The method of claim 12 wherein the contacting step is ina cell-free system.
 16. The method of claim 12 wherein polynucleotide iscoupled to a detectable label.
 17. The method of claim 12 wherein thetest compound is coupled to a detectable label.
 18. A method ofdiagnosing a disease selected from hematological diseases, disorders ofthe peripheral and central nervous system, gastrointestinal diseases,cardiovascular diseases, cancer, muscle/skeleton disorders, respiratorydiseases and urological diseases in a mammal comprising the steps of i)determining the amount of a 5-HT1F polynucleotide in a sample taken fromsaid mammal, ii) determining the amount of 5-HT1F polynucleotide inhealthy and/or diseased mammals.
 19. A pharmaceutical composition forthe treatment of a disease selected from hematological diseases,disorders of the peripheral and central nervous system, gastrointestinaldiseases, cardiovascular diseases, cancer, muscle/skeleton disorders,respiratory diseases and urological diseases in a mammal comprising atherapeutic agent which binds to a 5-HT1F polypeptide.
 20. Apharmaceutical composition for the treatment of a disease selected fromhematological diseases, disorders of the peripheral and central nervoussystem, gastrointestinal diseases, cardiovascular diseases, cancer,muscle/skeleton disorders, respiratory diseases and urological diseasesin a mammal comprising a therapeutic agent which regulates the activityof a 5-HT1F polypeptide.
 21. A pharmaceutical composition for thetreatment of a disease selected from hematological diseases, disordersof the peripheral and central nervous system, gastrointestinal diseases,cardiovascular diseases, cancer, muscle/skeleton disorders, respiratorydiseases and urological diseases in a mammal comprising a therapeuticagent which regulates the activity of a 5-HT1F polypeptide, wherein saidtherapeutic agent is i) a small molecule, ii) an RNA molecule, iii) anantisense oligonucleotide, iv) a polypeptide, v) an antibody, or vi) aribozyme.
 22. A pharmaceutical composition for the treatment of adisease selected from hematological diseases, disorders of theperipheral and central nervous system, gastrointestinal diseases,cardiovascular diseases, cancer, muscle/skeleton disorders, respiratorydiseases and urological diseases in a mammal comprising a 5-HT1Fpolynucleotide.
 23. A pharmaceutical composition for the treatment of adisease selected from hematological diseases, disorders of theperipheral and central nervous system, gastrointestinal diseases,cardiovascular diseases, cancer, muscle/skeleton disorders, respiratorydiseases and urological diseases in a mammal comprising a 5-HT1Fpolypeptide.
 24. A method for the treatment of a disease selected fromhematological diseases, disorders of the peripheral and central nervoussystem, gastrointestinal diseases, cardiovascular diseases, cancer,muscle/skeleton disorders, respiratory diseases and urological diseasesin a mammal comprising administering to a mammal an effective amount ofa regulator of 5-HT1F.
 25. Method for the preparation of apharmaceutical composition useful for the treatment of a diseaseselected from hematological diseases, disorders of the peripheral andcentral nervous system, gastrointestinal diseases, cardiovasculardiseases, cancer, muscle/skeleton disorders, respiratory diseases andurological diseases in a mammal comprising the steps of i) identifying aregulator of 5-HT1F, ii) determining whether said regulator amelioratesthe symptoms of a disease selected from hematological diseases,disorders of the peripheral and central nervous system, gastrointestinaldiseases, cardiovascular diseases, cancer, muscle/skeleton disorders,respiratory diseases and urological diseases in a mammal; and iii)combining of said regulator with an acceptable pharmaceutical carrier.26. A method for the regulation of 5-HT1F activity in a mammal having adisease selected from hematological diseases, disorders of theperipheral and central nervous system, gastrointestinal diseases,cardiovascular diseases, cancer, muscle/skeleton disorders, respiratorydiseases and urological diseases comprising administering to a mammal aneffective amount of a regulator of 5-HT1F.